From 3e0793fdd494b97cdf0591e88bb06a7ba6080b4e Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Tue, 30 Jul 2024 16:03:02 +0300 Subject: [PATCH 001/100] Install kraken2 and bracken --- modules.json | 10 ++ .../nf-core/bracken/bracken/environment.yml | 7 + modules/nf-core/bracken/bracken/main.nf | 52 ++++++ modules/nf-core/bracken/bracken/meta.yml | 51 ++++++ .../bracken/bracken/tests/main.nf.test | 121 ++++++++++++++ .../bracken/bracken/tests/main.nf.test.snap | 157 ++++++++++++++++++ .../bracken/bracken/tests/nextflow.config | 5 + .../nf-core/bracken/bracken/tests/tags.yml | 2 + .../nf-core/kraken2/kraken2/environment.yml | 9 + modules/nf-core/kraken2/kraken2/main.nf | 85 ++++++++++ modules/nf-core/kraken2/kraken2/meta.yml | 78 +++++++++ .../kraken2/kraken2/tests/main.nf.test | 143 ++++++++++++++++ .../kraken2/kraken2/tests/main.nf.test.snap | 74 +++++++++ .../nf-core/kraken2/kraken2/tests/tags.yml | 3 + 14 files changed, 797 insertions(+) create mode 100644 modules/nf-core/bracken/bracken/environment.yml create mode 100644 modules/nf-core/bracken/bracken/main.nf create mode 100644 modules/nf-core/bracken/bracken/meta.yml create mode 100644 modules/nf-core/bracken/bracken/tests/main.nf.test create mode 100644 modules/nf-core/bracken/bracken/tests/main.nf.test.snap create mode 100644 modules/nf-core/bracken/bracken/tests/nextflow.config create mode 100644 modules/nf-core/bracken/bracken/tests/tags.yml create mode 100644 modules/nf-core/kraken2/kraken2/environment.yml create mode 100644 modules/nf-core/kraken2/kraken2/main.nf create mode 100644 modules/nf-core/kraken2/kraken2/meta.yml create mode 100644 modules/nf-core/kraken2/kraken2/tests/main.nf.test create mode 100644 modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap create mode 100644 modules/nf-core/kraken2/kraken2/tests/tags.yml diff --git a/modules.json b/modules.json index f197e3f65..ac86bcd98 100644 --- a/modules.json +++ b/modules.json @@ -15,6 +15,11 @@ "git_sha": "81b90194ce9911dbd55bba2c65c6919f6677abc4", "installed_by": ["modules"] }, + "bracken/bracken": { + "branch": "master", + "git_sha": "f362bca32735a848feb314d601db1cee584ee0d1", + "installed_by": ["modules"] + }, "cat/fastq": { "branch": "master", "git_sha": "4fc983ad0b30e6e32696fa7d980c76c7bfe1c03e", @@ -90,6 +95,11 @@ "git_sha": "de5811dd9ca15af1e131806001bcaae909e42021", "installed_by": ["modules", "quantify_pseudo_alignment"] }, + "kraken2/kraken2": { + "branch": "master", + "git_sha": "ca87ad032a62f025f0c373facacef2df0c5411b2", + "installed_by": ["modules"] + }, "multiqc": { "branch": "master", "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396", diff --git a/modules/nf-core/bracken/bracken/environment.yml b/modules/nf-core/bracken/bracken/environment.yml new file mode 100644 index 000000000..6eb5b1b9a --- /dev/null +++ b/modules/nf-core/bracken/bracken/environment.yml @@ -0,0 +1,7 @@ +name: bracken_bracken +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::bracken=2.9" diff --git a/modules/nf-core/bracken/bracken/main.nf b/modules/nf-core/bracken/bracken/main.nf new file mode 100644 index 000000000..caded9edd --- /dev/null +++ b/modules/nf-core/bracken/bracken/main.nf @@ -0,0 +1,52 @@ +process BRACKEN_BRACKEN { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bracken:2.9--py38h2494328_0': + 'biocontainers/bracken:2.9--py38h2494328_0' }" + + input: + tuple val(meta), path(kraken_report) + path database + + output: + tuple val(meta), path(bracken_report) , emit: reports + tuple val(meta), path("*bracken_species.txt"), emit: txt + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: "" + def prefix = task.ext.prefix ?: "${meta.id}" + bracken_report = "${prefix}.tsv" + """ + bracken \\ + ${args} \\ + -d '${database}' \\ + -i '${kraken_report}' \\ + -o '${bracken_report}' + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bracken: \$(echo \$(bracken -v) | cut -f2 -d'v') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + bracken_report = "${prefix}.tsv" + """ + touch ${prefix}.tsv + touch ${prefix}_bracken_species.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bracken: \$(echo \$(bracken -v) | cut -f2 -d'v') + END_VERSIONS + """ +} diff --git a/modules/nf-core/bracken/bracken/meta.yml b/modules/nf-core/bracken/bracken/meta.yml new file mode 100644 index 000000000..b7ff4489f --- /dev/null +++ b/modules/nf-core/bracken/bracken/meta.yml @@ -0,0 +1,51 @@ +name: bracken_bracken +description: Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken. +keywords: + - bracken + - metagenomics + - abundance + - kraken2 +tools: + - bracken: + description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. + homepage: https://ccb.jhu.edu/software/bracken/ + documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual + tool_dev_url: https://github.com/jenniferlu717/Bracken + doi: "10.7717/peerj-cs.104" + licence: ["GPL v3"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - kraken_report: + type: file + description: TSV file with six columns coming from kraken2 output + pattern: "*.{tsv}" + - database: + type: file + description: Directory containing the kraken2/Bracken files for analysis + pattern: "*" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - reports: + type: file + description: TSV output report of the re-estimated abundances + pattern: "*.{tsv}" + - txt: + type: file + description: TXT file of bracken corrected results of Kraken2 report output + pattern: "*.txt" +authors: + - "@Midnighter" +maintainers: + - "@Midnighter" diff --git a/modules/nf-core/bracken/bracken/tests/main.nf.test b/modules/nf-core/bracken/bracken/tests/main.nf.test new file mode 100644 index 000000000..59c1398e5 --- /dev/null +++ b/modules/nf-core/bracken/bracken/tests/main.nf.test @@ -0,0 +1,121 @@ +nextflow_process { + + name "Test Process BRACKEN_BRACKEN" + script "../main.nf" + process "BRACKEN_BRACKEN" + + tag "modules" + tag "modules_nfcore" + tag "bracken" + tag "bracken/bracken" + tag "kraken2/kraken2" + tag "untar" + + setup { + run ("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = [[],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2_bracken.tar.gz', checkIfExists: true)] + """ + } + } + } + + test("sarscov2 - single-end - fastq") { + + setup { + run("KRAKEN2_KRAKEN2") { + script "../../../kraken2/kraken2/main.nf" + process { + """ + input[0] = [[id: 'test', single_end: true], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + input[1] = UNTAR.out.untar.map{it[1]} + input[2] = false + input[3] = false + """ + } + } + } + + when { + process { + """ + input[0] = KRAKEN2_KRAKEN2.out.report + input[1] = UNTAR.out.untar.map{it[1]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +test("sarscov2 - paired-end - fastq") { + + setup { + run("KRAKEN2_KRAKEN2") { + script "../../../kraken2/kraken2/main.nf" + process { + """ + input[0] = [ + [id: 'test', single_end: false], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ] + input[1] = UNTAR.out.untar.map{it[1]} + input[2] = false + input[3] = false + """ + } + } + } + + when { + process { + """ + input[0] = KRAKEN2_KRAKEN2.out.report + input[1] = UNTAR.out.untar.map{it[1]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - stub - fastq") { + + options "-stub" + + when { + process { + """ + input[0] = [[id: 'test'],file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true)] + input[1] = UNTAR.out.untar.map{it[1]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/bracken/bracken/tests/main.nf.test.snap b/modules/nf-core/bracken/bracken/tests/main.nf.test.snap new file mode 100644 index 000000000..5aadb7b70 --- /dev/null +++ b/modules/nf-core/bracken/bracken/tests/main.nf.test.snap @@ -0,0 +1,157 @@ +{ + "sarscov2 - single-end - fastq": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.tsv:md5,4a21ae14ff8a0311d55f139af5247838" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.kraken2.report_bracken_species.txt:md5,ca0fbeedc4353b5fdd081688823a33df" + ] + ], + "2": [ + "versions.yml:md5,599fbbf4c1cd5851022a98788f2afdba" + ], + "reports": [ + [ + { + "id": "test", + "single_end": true + }, + "test.tsv:md5,4a21ae14ff8a0311d55f139af5247838" + ] + ], + "txt": [ + [ + { + "id": "test", + "single_end": true + }, + "test.kraken2.report_bracken_species.txt:md5,ca0fbeedc4353b5fdd081688823a33df" + ] + ], + "versions": [ + "versions.yml:md5,599fbbf4c1cd5851022a98788f2afdba" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-04-16T14:14:27.122403998" + }, + "sarscov2 - paired-end - fastq": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,4a21ae14ff8a0311d55f139af5247838" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.kraken2.report_bracken_species.txt:md5,ca0fbeedc4353b5fdd081688823a33df" + ] + ], + "2": [ + "versions.yml:md5,599fbbf4c1cd5851022a98788f2afdba" + ], + "reports": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,4a21ae14ff8a0311d55f139af5247838" + ] + ], + "txt": [ + [ + { + "id": "test", + "single_end": false + }, + "test.kraken2.report_bracken_species.txt:md5,ca0fbeedc4353b5fdd081688823a33df" + ] + ], + "versions": [ + "versions.yml:md5,599fbbf4c1cd5851022a98788f2afdba" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-04-16T14:19:15.627050252" + }, + "sarscov2 - stub - fastq": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test_bracken_species.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,599fbbf4c1cd5851022a98788f2afdba" + ], + "reports": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "txt": [ + [ + { + "id": "test" + }, + "test_bracken_species.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,599fbbf4c1cd5851022a98788f2afdba" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-04-16T14:14:36.5929911" + } +} \ No newline at end of file diff --git a/modules/nf-core/bracken/bracken/tests/nextflow.config b/modules/nf-core/bracken/bracken/tests/nextflow.config new file mode 100644 index 000000000..b550b7489 --- /dev/null +++ b/modules/nf-core/bracken/bracken/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: BRACKEN_BRACKEN { + ext.args = "-l S -t 10 -r 150" + } +} diff --git a/modules/nf-core/bracken/bracken/tests/tags.yml b/modules/nf-core/bracken/bracken/tests/tags.yml new file mode 100644 index 000000000..6a2cbd384 --- /dev/null +++ b/modules/nf-core/bracken/bracken/tests/tags.yml @@ -0,0 +1,2 @@ +bracken/bracken: + - "modules/nf-core/bracken/bracken/**" diff --git a/modules/nf-core/kraken2/kraken2/environment.yml b/modules/nf-core/kraken2/kraken2/environment.yml new file mode 100644 index 000000000..0c067feeb --- /dev/null +++ b/modules/nf-core/kraken2/kraken2/environment.yml @@ -0,0 +1,9 @@ +name: kraken2_kraken2 +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::kraken2=2.1.3" + - "coreutils=9.4" + - "pigz=2.8" diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf new file mode 100644 index 000000000..364a6fe24 --- /dev/null +++ b/modules/nf-core/kraken2/kraken2/main.nf @@ -0,0 +1,85 @@ +process KRAKEN2_KRAKEN2 { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-8706a1dd73c6cc426e12dd4dd33a5e917b3989ae:c8cbdc8ff4101e6745f8ede6eb5261ef98bdaff4-0' : + 'biocontainers/mulled-v2-8706a1dd73c6cc426e12dd4dd33a5e917b3989ae:c8cbdc8ff4101e6745f8ede6eb5261ef98bdaff4-0' }" + + input: + tuple val(meta), path(reads) + path db + val save_output_fastqs + val save_reads_assignment + + output: + tuple val(meta), path('*.classified{.,_}*') , optional:true, emit: classified_reads_fastq + tuple val(meta), path('*.unclassified{.,_}*') , optional:true, emit: unclassified_reads_fastq + tuple val(meta), path('*classifiedreads.txt') , optional:true, emit: classified_reads_assignment + tuple val(meta), path('*report.txt') , emit: report + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def paired = meta.single_end ? "" : "--paired" + def classified = meta.single_end ? "${prefix}.classified.fastq" : "${prefix}.classified#.fastq" + def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq" + def classified_option = save_output_fastqs ? "--classified-out ${classified}" : "" + def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : "" + def readclassification_option = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : "--output /dev/null" + def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : "" + + """ + kraken2 \\ + --db $db \\ + --threads $task.cpus \\ + --report ${prefix}.kraken2.report.txt \\ + --gzip-compressed \\ + $unclassified_option \\ + $classified_option \\ + $readclassification_option \\ + $paired \\ + $args \\ + $reads + + $compress_reads_command + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//') + pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def paired = meta.single_end ? "" : "--paired" + def classified = meta.single_end ? "${prefix}.classified.fastq.gz" : "${prefix}.classified_1.fastq.gz ${prefix}.classified_2.fastq.gz" + def unclassified = meta.single_end ? "${prefix}.unclassified.fastq.gz" : "${prefix}.unclassified_1.fastq.gz ${prefix}.unclassified_2.fastq.gz" + def readclassification_option = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : "--output /dev/null" + def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : "" + + """ + touch ${prefix}.kraken2.report.txt + if [ "$save_output_fastqs" == "true" ]; then + touch $classified + touch $unclassified + fi + if [ "$save_reads_assignment" == "true" ]; then + touch ${prefix}.kraken2.classifiedreads.txt + fi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//') + pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) + END_VERSIONS + """ + +} diff --git a/modules/nf-core/kraken2/kraken2/meta.yml b/modules/nf-core/kraken2/kraken2/meta.yml new file mode 100644 index 000000000..7909ffe7e --- /dev/null +++ b/modules/nf-core/kraken2/kraken2/meta.yml @@ -0,0 +1,78 @@ +name: kraken2_kraken2 +description: Classifies metagenomic sequence data +keywords: + - classify + - metagenomics + - fastq + - db +tools: + - kraken2: + description: | + Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to sequence reads + homepage: https://ccb.jhu.edu/software/kraken2/ + documentation: https://github.com/DerrickWood/kraken2/wiki/Manual + doi: 10.1186/s13059-019-1891-0 + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - db: + type: directory + description: Kraken2 database + - save_output_fastqs: + type: string + description: | + If true, optional commands are added to save classified and unclassified reads + as fastq files + - save_reads_assignment: + type: string + description: | + If true, an optional command is added to save a file reporting the taxonomic + classification of each input read +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - classified_reads_fastq: + type: file + description: | + Reads classified as belonging to any of the taxa + on the Kraken2 database. + pattern: "*{fastq.gz}" + - unclassified_reads_fastq: + type: file + description: | + Reads not classified to any of the taxa + on the Kraken2 database. + pattern: "*{fastq.gz}" + - classified_reads_assignment: + type: file + description: | + Kraken2 output file indicating the taxonomic assignment of + each input read + - report: + type: file + description: | + Kraken2 report containing stats about classified + and not classifed reads. + pattern: "*.{report.txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@joseespinosa" + - "@drpatelh" +maintainers: + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/kraken2/kraken2/tests/main.nf.test b/modules/nf-core/kraken2/kraken2/tests/main.nf.test new file mode 100644 index 000000000..4c5130217 --- /dev/null +++ b/modules/nf-core/kraken2/kraken2/tests/main.nf.test @@ -0,0 +1,143 @@ +nextflow_process { + name "Test Process KRAKEN2_KRAKEN2" + script "../main.nf" + process "KRAKEN2_KRAKEN2" + tag "modules" + tag "modules_nfcore" + tag "untar" + tag "kraken2" + tag "kraken2/kraken2" + + setup { + run("UNTAR") { + script "modules/nf-core/untar/main.nf" + process { + """ + input[0] = Channel.of([ + [], + file( + params.test_data['sarscov2']['genome']['kraken2_tar_gz'], + checkIfExists: true + ) + ]) + """ + } + } + } + + test("sarscov2 illumina single end [fastq]") { + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + [ file( + params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], + checkIfExists: true + )] + ] + input[1] = UNTAR.out.untar.map{ it[1] } + input[2] = true + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.report, + process.out.versions, + ).match() + }, + { assert process.out.classified_reads_fastq.get(0).get(1) ==~ ".*/test.classified.fastq.gz" }, + { assert process.out.unclassified_reads_fastq.get(0).get(1) ==~ ".*/test.unclassified.fastq.gz" }, + ) + } + } + + test("sarscov2 illumina paired end [fastq]") { + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file( + params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], + checkIfExists: true + ), + file( + params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], + checkIfExists: true + ) + + ] + ] + input[1] = UNTAR.out.untar.map{ it[1] } + input[2] = true + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.report, + process.out.versions, + ).match() + }, + { assert process.out.classified_reads_fastq.get(0).get(1).get(0) + ==~ ".*/test.classified_1.fastq.gz" }, + { assert process.out.classified_reads_fastq.get(0).get(1).get(1) + ==~ ".*/test.classified_2.fastq.gz" }, + { assert process.out.unclassified_reads_fastq.get(0).get(1).get(0) + ==~ ".*/test.unclassified_1.fastq.gz" }, + { assert process.out.unclassified_reads_fastq.get(0).get(1).get(1) + ==~ ".*/test.unclassified_2.fastq.gz" }, + ) + } + } + + test("sarscov2 illumina single end [fastq] + save_reads_assignment") { + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + [ file( + params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], + checkIfExists: true + )] + ] + input[1] = UNTAR.out.untar.map{ it[1] } + input[2] = false + input[3] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.report, + process.out.classified_reads_assignment, + process.out.versions, + ).match() + }, + ) + } + } +} diff --git a/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap b/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap new file mode 100644 index 000000000..b432f878f --- /dev/null +++ b/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap @@ -0,0 +1,74 @@ +{ + "sarscov2 illumina single end [fastq]": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e" + ] + ], + [ + "versions.yml:md5,79adf2ca1cfc625cb77e391b27142c43" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-04T18:47:03.745692" + }, + "sarscov2 illumina paired end [fastq]": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e" + ] + ], + [ + "versions.yml:md5,79adf2ca1cfc625cb77e391b27142c43" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-04T18:47:13.75649" + }, + "sarscov2 illumina single end [fastq] + save_reads_assignment": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.kraken2.classifiedreads.txt:md5,e7a90531f0d8d777316515c36fe4cae0" + ] + ], + [ + "versions.yml:md5,79adf2ca1cfc625cb77e391b27142c43" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-04T18:47:22.459465" + } +} \ No newline at end of file diff --git a/modules/nf-core/kraken2/kraken2/tests/tags.yml b/modules/nf-core/kraken2/kraken2/tests/tags.yml new file mode 100644 index 000000000..9ebfd7ab6 --- /dev/null +++ b/modules/nf-core/kraken2/kraken2/tests/tags.yml @@ -0,0 +1,3 @@ +kraken2/kraken2: + - modules/nf-core/kraken2/kraken2/** + - modules/nf-core/untar/** From a7281e5ed53903d44bb6c5ad272f68834e067eb0 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Tue, 30 Jul 2024 16:12:13 +0300 Subject: [PATCH 002/100] Change nextflow configurations --- modules/nf-core/bracken/bracken/nextflow.config | 11 +++++++++++ modules/nf-core/kraken2/kraken2/nextflow.config | 13 +++++++++++++ nextflow.config | 5 ++++- 3 files changed, 28 insertions(+), 1 deletion(-) create mode 100644 modules/nf-core/bracken/bracken/nextflow.config create mode 100644 modules/nf-core/kraken2/kraken2/nextflow.config diff --git a/modules/nf-core/bracken/bracken/nextflow.config b/modules/nf-core/bracken/bracken/nextflow.config new file mode 100644 index 000000000..8089e551f --- /dev/null +++ b/modules/nf-core/bracken/bracken/nextflow.config @@ -0,0 +1,11 @@ +if (!params.skip_alignment && !params.skip_qc) { + if (!params.skip_kraken2) { + withName: 'BRACKEN' { + ext.args = "-l ${params.bracken_precision}" + publishDir = [ + path: { "${params.outdir}/bracken" }, + mode: params.publish_dir_mode + ] + } + } +} \ No newline at end of file diff --git a/modules/nf-core/kraken2/kraken2/nextflow.config b/modules/nf-core/kraken2/kraken2/nextflow.config new file mode 100644 index 000000000..a81d68de3 --- /dev/null +++ b/modules/nf-core/kraken2/kraken2/nextflow.config @@ -0,0 +1,13 @@ +if (!params.skip_alignment && !params.skip_qc) { + if (!params.skip_kraken2) { + process { + withName: 'KRAKEN2' { + ext.args = "--confidence 0.05 --minimum-hit-groups 3" + publishDir = [ + path: { "${params.outdir}/kraken2/kraken_reports" }, + mode: params.publish_dir_mode + ] + } + } + } +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 1c46d7c2e..47833626c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -73,7 +73,7 @@ params { kallisto_quant_fraglen = 200 kallisto_quant_fraglen_sd = 200 save_merged_fastq = false - save_unaligned = false + save_unaligned = true save_align_intermeds = false skip_markduplicates = false skip_alignment = false @@ -89,6 +89,9 @@ params { skip_preseq = true skip_dupradar = false skip_qualimap = false + skip_kraken2 = false + kraken_db = null + bracken_precision = "G" skip_rseqc = false skip_biotype_qc = false skip_deseq2_qc = false From 734919e309047f46c46fae6848fb128bd4323d4b Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Tue, 30 Jul 2024 16:31:40 +0300 Subject: [PATCH 003/100] Initial addition of kraken and bracken to pipeline --- workflows/rnaseq/main.nf | 41 +++++++++++++++++++++++++++++++--------- 1 file changed, 32 insertions(+), 9 deletions(-) diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index 7bf5d36e0..b86079c1b 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -38,6 +38,8 @@ include { PRESEQ_LCEXTRAP } from '../../modules/nf-core/preseq/lcextrap' include { QUALIMAP_RNASEQ } from '../../modules/nf-core/qualimap/rnaseq' include { STRINGTIE_STRINGTIE } from '../../modules/nf-core/stringtie/stringtie' include { SUBREAD_FEATURECOUNTS } from '../../modules/nf-core/subread/featurecounts' +include { KRAKEN2_BUILD } from '../modules/nf-core/kraken2/build/main' +include { BRACKEN_BUILD } from '../modules/nf-core/bracken/build/main' include { MULTIQC } from '../../modules/nf-core/multiqc' include { UMITOOLS_PREPAREFORRSEM as UMITOOLS_PREPAREFORSALMON } from '../../modules/nf-core/umitools/prepareforrsem' include { BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_FW } from '../../modules/nf-core/bedtools/genomecov' @@ -158,9 +160,10 @@ workflow RNASEQ { // // SUBWORKFLOW: Alignment with STAR and gene/transcript quantification with Salmon // - ch_genome_bam = Channel.empty() - ch_genome_bam_index = Channel.empty() - ch_star_log = Channel.empty() + ch_genome_bam = Channel.empty() + ch_genome_bam_index = Channel.empty() + ch_star_log = Channel.empty() + ch_unaligned_sequences = Channel.empty() if (!params.skip_alignment && params.aligner == 'star_salmon') { // Check if an AWS iGenome has been provided to use the appropriate version of STAR def is_aws_igenome = false @@ -180,10 +183,11 @@ workflow RNASEQ { is_aws_igenome, ch_fasta.map { [ [:], it ] } ) - ch_genome_bam = ALIGN_STAR.out.bam - ch_genome_bam_index = ALIGN_STAR.out.bai - ch_transcriptome_bam = ALIGN_STAR.out.bam_transcript - ch_star_log = ALIGN_STAR.out.log_final + ch_genome_bam = ALIGN_STAR.out.bam + ch_genome_bam_index = ALIGN_STAR.out.bai + ch_transcriptome_bam = ALIGN_STAR.out.bam_transcript + ch_star_log = ALIGN_STAR.out.log_final + ch_unaligned_sequences = ALIGN_STAR.out.fastq ch_multiqc_files = ch_multiqc_files.mix(ALIGN_STAR.out.stats.collect{it[1]}) ch_multiqc_files = ch_multiqc_files.mix(ALIGN_STAR.out.flagstat.collect{it[1]}) ch_multiqc_files = ch_multiqc_files.mix(ALIGN_STAR.out.idxstats.collect{it[1]}) @@ -337,8 +341,9 @@ workflow RNASEQ { ch_splicesites.map { [ [:], it ] }, ch_fasta.map { [ [:], it ] } ) - ch_genome_bam = FASTQ_ALIGN_HISAT2.out.bam - ch_genome_bam_index = FASTQ_ALIGN_HISAT2.out.bai + ch_genome_bam = FASTQ_ALIGN_HISAT2.out.bam + ch_genome_bam_index = FASTQ_ALIGN_HISAT2.out.bai + ch_unaligned_sequences = FASTQ_ALIGN_HISAT2.out.fastq ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_HISAT2.out.stats.collect{it[1]}) ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_HISAT2.out.flagstat.collect{it[1]}) ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_HISAT2.out.idxstats.collect{it[1]}) @@ -634,6 +639,24 @@ workflow RNASEQ { ch_multiqc_files = ch_multiqc_files.mix(ch_fail_strand_multiqc.collectFile(name: 'fail_strand_check_mqc.tsv')) } + + if (!params.skip_kraken2) { + KRAKEN2 ( + ch_unaligned_sequences, + params.kraken_db, + false, //TODO Not saving read alignments. Should this be modifiable? + false + ) + ch_kraken_reports = KRAKEN2.out.report + ch_versions = ch_versions.mix(KRAKEN2.out.versions) + + BRACKEN ( + ch_kraken_reports, + kraken_db + ) + ch_versions = ch_versions.mix(BRACKEN.out.versions) + ch_multiqc_files = ch_multiqc_files.mix(BRACKEN.out.reports.collect().ifEmpty([])) + } } // From 8695f5093b7e2a02ed3f7dd6b53ff90607d0e2a5 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Wed, 31 Jul 2024 10:38:30 +0300 Subject: [PATCH 004/100] Fix include statements --- workflows/rnaseq/main.nf | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index b86079c1b..a514c05b0 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -32,15 +32,15 @@ include { getInferexperimentStrandedness } from '../../subworkflows/local/utils_ // // MODULE: Installed directly from nf-core/modules // -include { DUPRADAR } from '../../modules/nf-core/dupradar' -include { SAMTOOLS_SORT } from '../../modules/nf-core/samtools/sort' -include { PRESEQ_LCEXTRAP } from '../../modules/nf-core/preseq/lcextrap' -include { QUALIMAP_RNASEQ } from '../../modules/nf-core/qualimap/rnaseq' -include { STRINGTIE_STRINGTIE } from '../../modules/nf-core/stringtie/stringtie' -include { SUBREAD_FEATURECOUNTS } from '../../modules/nf-core/subread/featurecounts' -include { KRAKEN2_BUILD } from '../modules/nf-core/kraken2/build/main' -include { BRACKEN_BUILD } from '../modules/nf-core/bracken/build/main' -include { MULTIQC } from '../../modules/nf-core/multiqc' +include { DUPRADAR } from '../../modules/nf-core/dupradar' +include { SAMTOOLS_SORT } from '../../modules/nf-core/samtools/sort' +include { PRESEQ_LCEXTRAP } from '../../modules/nf-core/preseq/lcextrap' +include { QUALIMAP_RNASEQ } from '../../modules/nf-core/qualimap/rnaseq' +include { STRINGTIE_STRINGTIE } from '../../modules/nf-core/stringtie/stringtie' +include { SUBREAD_FEATURECOUNTS } from '../../modules/nf-core/subread/featurecounts' +include { KRAKEN2_KRAKEN2 as KRAKEN2 } from '../modules/nf-core/kraken2/kraken2/main' +include { BRACKEN_BRACKEN as BRACKEN } from '../modules/nf-core/bracken/bracken/main' +include { MULTIQC } from '../../modules/nf-core/multiqc' include { UMITOOLS_PREPAREFORRSEM as UMITOOLS_PREPAREFORSALMON } from '../../modules/nf-core/umitools/prepareforrsem' include { BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_FW } from '../../modules/nf-core/bedtools/genomecov' include { BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_REV } from '../../modules/nf-core/bedtools/genomecov' From 44ba28282edc17586b8395c1018f05e3f6067daa Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Wed, 31 Jul 2024 16:10:43 +0300 Subject: [PATCH 005/100] Fix include statements --- workflows/rnaseq/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index a514c05b0..d7602e2a6 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -38,8 +38,8 @@ include { PRESEQ_LCEXTRAP } from '../../modules/nf-core/preseq/lcextr include { QUALIMAP_RNASEQ } from '../../modules/nf-core/qualimap/rnaseq' include { STRINGTIE_STRINGTIE } from '../../modules/nf-core/stringtie/stringtie' include { SUBREAD_FEATURECOUNTS } from '../../modules/nf-core/subread/featurecounts' -include { KRAKEN2_KRAKEN2 as KRAKEN2 } from '../modules/nf-core/kraken2/kraken2/main' -include { BRACKEN_BRACKEN as BRACKEN } from '../modules/nf-core/bracken/bracken/main' +include { KRAKEN2_KRAKEN2 as KRAKEN2 } from '../../modules/nf-core/kraken2/kraken2/main' +include { BRACKEN_BRACKEN as BRACKEN } from '../../modules/nf-core/bracken/bracken/main' include { MULTIQC } from '../../modules/nf-core/multiqc' include { UMITOOLS_PREPAREFORRSEM as UMITOOLS_PREPAREFORSALMON } from '../../modules/nf-core/umitools/prepareforrsem' include { BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_FW } from '../../modules/nf-core/bedtools/genomecov' @@ -652,7 +652,7 @@ workflow RNASEQ { BRACKEN ( ch_kraken_reports, - kraken_db + params.kraken_db ) ch_versions = ch_versions.mix(BRACKEN.out.versions) ch_multiqc_files = ch_multiqc_files.mix(BRACKEN.out.reports.collect().ifEmpty([])) From 3657e3e7eca46588c108ecb1daad8f511db82072 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Mon, 5 Aug 2024 10:23:21 +0300 Subject: [PATCH 006/100] Include module config files --- workflows/rnaseq/nextflow.config | 2 ++ 1 file changed, 2 insertions(+) diff --git a/workflows/rnaseq/nextflow.config b/workflows/rnaseq/nextflow.config index c7eeac733..9cbf0cd30 100644 --- a/workflows/rnaseq/nextflow.config +++ b/workflows/rnaseq/nextflow.config @@ -8,6 +8,8 @@ includeConfig "../../modules/nf-core/qualimap/rnaseq/nextflow.config" includeConfig "../../modules/nf-core/sortmerna/nextflow.config" includeConfig "../../modules/nf-core/stringtie/stringtie/nextflow.config" includeConfig "../../modules/nf-core/subread/featurecounts/nextflow.config" +includeConfig "../../modules/nf-core/kraken2/kraken2/nextflow.config" +includeConfig "../../modules/nf-core/bracken/bracken/nextflow.config" includeConfig "../../subworkflows/local/align_star/nextflow.config" includeConfig "../../subworkflows/local/quantify_rsem/nextflow.config" includeConfig "../../subworkflows/nf-core/quantify_pseudo_alignment/nextflow.config" From 7ab90f670bf6ee7ef580eb16ac6b0a1740ed49c1 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Mon, 5 Aug 2024 10:23:51 +0300 Subject: [PATCH 007/100] Use presence of kraken_db to determine bracken run, add save params --- .../nf-core/bracken/bracken/nextflow.config | 2 +- .../nf-core/kraken2/kraken2/nextflow.config | 2 +- nextflow.config | 4 ++- workflows/rnaseq/main.nf | 25 ++++++++++++------- 4 files changed, 21 insertions(+), 12 deletions(-) diff --git a/modules/nf-core/bracken/bracken/nextflow.config b/modules/nf-core/bracken/bracken/nextflow.config index 8089e551f..cf7b1cad6 100644 --- a/modules/nf-core/bracken/bracken/nextflow.config +++ b/modules/nf-core/bracken/bracken/nextflow.config @@ -1,5 +1,5 @@ if (!params.skip_alignment && !params.skip_qc) { - if (!params.skip_kraken2) { + if (params.kraken_db && !params.skip_bracken) { withName: 'BRACKEN' { ext.args = "-l ${params.bracken_precision}" publishDir = [ diff --git a/modules/nf-core/kraken2/kraken2/nextflow.config b/modules/nf-core/kraken2/kraken2/nextflow.config index a81d68de3..0070ad9fd 100644 --- a/modules/nf-core/kraken2/kraken2/nextflow.config +++ b/modules/nf-core/kraken2/kraken2/nextflow.config @@ -1,5 +1,5 @@ if (!params.skip_alignment && !params.skip_qc) { - if (!params.skip_kraken2) { + if (params.kraken_db) { process { withName: 'KRAKEN2' { ext.args = "--confidence 0.05 --minimum-hit-groups 3" diff --git a/nextflow.config b/nextflow.config index 47833626c..5e2d8a9f2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -89,8 +89,10 @@ params { skip_preseq = true skip_dupradar = false skip_qualimap = false - skip_kraken2 = false kraken_db = null + skip_bracken = false + save_kraken_assignments = false + save_kraken_unassigned = false bracken_precision = "G" skip_rseqc = false skip_biotype_qc = false diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index d7602e2a6..e5aeff0a1 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -640,22 +640,29 @@ workflow RNASEQ { ch_multiqc_files = ch_multiqc_files.mix(ch_fail_strand_multiqc.collectFile(name: 'fail_strand_check_mqc.tsv')) } - if (!params.skip_kraken2) { + if (params.kraken_db) { KRAKEN2 ( ch_unaligned_sequences, params.kraken_db, - false, //TODO Not saving read alignments. Should this be modifiable? - false + params.save_kraken_assignments, + params.save_kraken_unassigned ) ch_kraken_reports = KRAKEN2.out.report ch_versions = ch_versions.mix(KRAKEN2.out.versions) - BRACKEN ( - ch_kraken_reports, - params.kraken_db - ) - ch_versions = ch_versions.mix(BRACKEN.out.versions) - ch_multiqc_files = ch_multiqc_files.mix(BRACKEN.out.reports.collect().ifEmpty([])) + // Only put Kraken2 output in MultiQC if Bracken is not run + if (params.skip_bracken) { + ch_multiqc_files = ch_multiqc_files.mix(KRAKEN2.out.reports.collect{it[1]}.ifEmpty([])) + } + + if (!params.skip_bracken) { + BRACKEN ( + ch_kraken_reports, + params.kraken_db + ) + ch_versions = ch_versions.mix(BRACKEN.out.versions) + ch_multiqc_files = ch_multiqc_files.mix(BRACKEN.out.reports.collect{it[1]}.ifEmpty([])) + } } } From 39cfdef38a9b3ba44c40b652cd0680c5ff6f146d Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Mon, 5 Aug 2024 16:24:38 +0300 Subject: [PATCH 008/100] Fix multiqc for Bracken/Kraken --- workflows/rnaseq/assets/multiqc/multiqc_config.yml | 8 ++++++++ workflows/rnaseq/main.nf | 4 ++-- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml index 2bf39b16c..5d144cbdf 100644 --- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml +++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml @@ -30,6 +30,8 @@ run_modules: - preseq - rseqc - qualimap + - kraken + - bracken # Order of modules top_modules: @@ -105,6 +107,12 @@ sp: samtools/idxstats: fn: "*.idxstats*" + kraken: + fn: "*report.txt" + + bracken: + fn: "*bracken_species.txt" + rseqc/bam_stat: fn: "*.bam_stat.txt" rseqc/gene_body_coverage: diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index e5aeff0a1..323db5d02 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -652,7 +652,7 @@ workflow RNASEQ { // Only put Kraken2 output in MultiQC if Bracken is not run if (params.skip_bracken) { - ch_multiqc_files = ch_multiqc_files.mix(KRAKEN2.out.reports.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(KRAKEN2.out.report.collect{it[1]}) } if (!params.skip_bracken) { @@ -661,7 +661,7 @@ workflow RNASEQ { params.kraken_db ) ch_versions = ch_versions.mix(BRACKEN.out.versions) - ch_multiqc_files = ch_multiqc_files.mix(BRACKEN.out.reports.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(BRACKEN.out.txt.collect{it[1]}) } } } From 2e9c24398f2fbc76920dc389284b2b42ee41a952 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Mon, 5 Aug 2024 16:31:44 +0300 Subject: [PATCH 009/100] Add Bracken/Kraken citations --- CITATIONS.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/CITATIONS.md b/CITATIONS.md index 48a60b8e4..5eaeea7f8 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -16,6 +16,10 @@ > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824. +- [Bracken](https://doi.org/10.7717/peerj-cs.104) + + > Lu, J., Breitwieser, F. P., Thielen, P., & Salzberg, S. L. (2017). Bracken: estimating species abundance in metagenomics data. PeerJ. Computer Science, 3(e104), e104. https://doi.org/10.7717/peerj-cs.104 + - [fastp](https://www.ncbi.nlm.nih.gov/pubmed/30423086/) > Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PubMed PMID: 30423086; PubMed Central PMCID: PMC6129281. @@ -38,6 +42,10 @@ > Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4. Epub 2019 Aug 2. PubMed PMID: 31375807. +- [Kraken2](https://doi.org/10.1186/s13059-019-1891-0) + + > Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. https://doi.org/10.1186/s13059-019-1891-0 + - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. From 03314c9b280b6af42d4658f94a4736d079945a5b Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Tue, 6 Aug 2024 12:49:33 +0300 Subject: [PATCH 010/100] Fix bracken config --- modules/nf-core/bracken/bracken/nextflow.config | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/bracken/bracken/nextflow.config b/modules/nf-core/bracken/bracken/nextflow.config index cf7b1cad6..e6d396652 100644 --- a/modules/nf-core/bracken/bracken/nextflow.config +++ b/modules/nf-core/bracken/bracken/nextflow.config @@ -1,11 +1,13 @@ if (!params.skip_alignment && !params.skip_qc) { if (params.kraken_db && !params.skip_bracken) { - withName: 'BRACKEN' { - ext.args = "-l ${params.bracken_precision}" - publishDir = [ - path: { "${params.outdir}/bracken" }, - mode: params.publish_dir_mode - ] + process { + withName: 'BRACKEN' { + ext.args = "-l ${params.bracken_precision}" + publishDir = [ + path: { "${params.outdir}/bracken" }, + mode: params.publish_dir_mode + ] + } } } } \ No newline at end of file From 7913cbca1cf060fdc37b000f249dec57a089cb28 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Wed, 7 Aug 2024 07:37:08 +0000 Subject: [PATCH 011/100] Update bracken --- modules.json | 2 +- modules/nf-core/bracken/bracken/main.nf | 9 +- .../bracken/bracken/tests/genus_test.config | 5 ++ .../bracken/bracken/tests/main.nf.test | 48 ++++++++++- .../bracken/bracken/tests/main.nf.test.snap | 83 +++++++++++++++---- 5 files changed, 127 insertions(+), 20 deletions(-) create mode 100644 modules/nf-core/bracken/bracken/tests/genus_test.config diff --git a/modules.json b/modules.json index ac86bcd98..20b52c3a1 100644 --- a/modules.json +++ b/modules.json @@ -17,7 +17,7 @@ }, "bracken/bracken": { "branch": "master", - "git_sha": "f362bca32735a848feb314d601db1cee584ee0d1", + "git_sha": "c214fad97b328eb6d6233f779be9ba44814a9136", "installed_by": ["modules"] }, "cat/fastq": { diff --git a/modules/nf-core/bracken/bracken/main.nf b/modules/nf-core/bracken/bracken/main.nf index caded9edd..e3d32fb21 100644 --- a/modules/nf-core/bracken/bracken/main.nf +++ b/modules/nf-core/bracken/bracken/main.nf @@ -13,7 +13,7 @@ process BRACKEN_BRACKEN { output: tuple val(meta), path(bracken_report) , emit: reports - tuple val(meta), path("*bracken_species.txt"), emit: txt + tuple val(meta), path(bracken_kraken_style_report), emit: txt path "versions.yml" , emit: versions when: @@ -23,12 +23,14 @@ process BRACKEN_BRACKEN { def args = task.ext.args ?: "" def prefix = task.ext.prefix ?: "${meta.id}" bracken_report = "${prefix}.tsv" + bracken_kraken_style_report = "${prefix}.kraken2.report_bracken.txt" """ bracken \\ ${args} \\ -d '${database}' \\ -i '${kraken_report}' \\ - -o '${bracken_report}' + -o '${bracken_report}' \\ + -w '${bracken_kraken_style_report}' cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -40,9 +42,10 @@ process BRACKEN_BRACKEN { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" bracken_report = "${prefix}.tsv" + bracken_kraken_style_report = "${prefix}.kraken2.report_bracken.txt" """ touch ${prefix}.tsv - touch ${prefix}_bracken_species.txt + touch ${bracken_kraken_style_report} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bracken/bracken/tests/genus_test.config b/modules/nf-core/bracken/bracken/tests/genus_test.config new file mode 100644 index 000000000..bc5f63ae0 --- /dev/null +++ b/modules/nf-core/bracken/bracken/tests/genus_test.config @@ -0,0 +1,5 @@ +process { + withName: BRACKEN_BRACKEN { + ext.args = "-l G -t 10 -r 150" + } +} diff --git a/modules/nf-core/bracken/bracken/tests/main.nf.test b/modules/nf-core/bracken/bracken/tests/main.nf.test index 59c1398e5..9d2105ded 100644 --- a/modules/nf-core/bracken/bracken/tests/main.nf.test +++ b/modules/nf-core/bracken/bracken/tests/main.nf.test @@ -24,6 +24,8 @@ nextflow_process { test("sarscov2 - single-end - fastq") { + config "./nextflow.config" + setup { run("KRAKEN2_KRAKEN2") { script "../../../kraken2/kraken2/main.nf" @@ -56,7 +58,51 @@ nextflow_process { } -test("sarscov2 - paired-end - fastq") { + test("sarscov2 - paired-end - fastq - genus config") { + + config "./genus_test.config" + + setup { + run("KRAKEN2_KRAKEN2") { + script "../../../kraken2/kraken2/main.nf" + process { + """ + input[0] = [ + [id: 'test', single_end: false], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ] + input[1] = UNTAR.out.untar.map{it[1]} + input[2] = false + input[3] = false + """ + } + } + } + + when { + process { + """ + input[0] = KRAKEN2_KRAKEN2.out.report + input[1] = UNTAR.out.untar.map{it[1]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - paired-end - fastq") { + + config "./nextflow.config" setup { run("KRAKEN2_KRAKEN2") { diff --git a/modules/nf-core/bracken/bracken/tests/main.nf.test.snap b/modules/nf-core/bracken/bracken/tests/main.nf.test.snap index 5aadb7b70..c97a4c71b 100644 --- a/modules/nf-core/bracken/bracken/tests/main.nf.test.snap +++ b/modules/nf-core/bracken/bracken/tests/main.nf.test.snap @@ -17,7 +17,7 @@ "id": "test", "single_end": true }, - "test.kraken2.report_bracken_species.txt:md5,ca0fbeedc4353b5fdd081688823a33df" + "test.kraken2.report_bracken.txt:md5,ca0fbeedc4353b5fdd081688823a33df" ] ], "2": [ @@ -38,7 +38,7 @@ "id": "test", "single_end": true }, - "test.kraken2.report_bracken_species.txt:md5,ca0fbeedc4353b5fdd081688823a33df" + "test.kraken2.report_bracken.txt:md5,ca0fbeedc4353b5fdd081688823a33df" ] ], "versions": [ @@ -47,10 +47,63 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-04-16T14:14:27.122403998" + "timestamp": "2024-08-06T11:35:03.995620397" + }, + "sarscov2 - paired-end - fastq - genus config": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,f609b09d6edb5ebc1ea1435d1dd46cde" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.kraken2.report_bracken.txt:md5,2ce58814420a3690da1f08e10e8d3a30" + ] + ], + "2": [ + "versions.yml:md5,599fbbf4c1cd5851022a98788f2afdba" + ], + "reports": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,f609b09d6edb5ebc1ea1435d1dd46cde" + ] + ], + "txt": [ + [ + { + "id": "test", + "single_end": false + }, + "test.kraken2.report_bracken.txt:md5,2ce58814420a3690da1f08e10e8d3a30" + ] + ], + "versions": [ + "versions.yml:md5,599fbbf4c1cd5851022a98788f2afdba" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-06T12:13:33.399680181" }, "sarscov2 - paired-end - fastq": { "content": [ @@ -70,7 +123,7 @@ "id": "test", "single_end": false }, - "test.kraken2.report_bracken_species.txt:md5,ca0fbeedc4353b5fdd081688823a33df" + "test.kraken2.report_bracken.txt:md5,ca0fbeedc4353b5fdd081688823a33df" ] ], "2": [ @@ -91,7 +144,7 @@ "id": "test", "single_end": false }, - "test.kraken2.report_bracken_species.txt:md5,ca0fbeedc4353b5fdd081688823a33df" + "test.kraken2.report_bracken.txt:md5,ca0fbeedc4353b5fdd081688823a33df" ] ], "versions": [ @@ -100,10 +153,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-04-16T14:19:15.627050252" + "timestamp": "2024-08-06T12:09:15.465609745" }, "sarscov2 - stub - fastq": { "content": [ @@ -121,7 +174,7 @@ { "id": "test" }, - "test_bracken_species.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.kraken2.report_bracken.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ @@ -140,7 +193,7 @@ { "id": "test" }, - "test_bracken_species.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.kraken2.report_bracken.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ @@ -149,9 +202,9 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-04-16T14:14:36.5929911" + "timestamp": "2024-08-06T11:35:42.965471207" } } \ No newline at end of file From 063b4ac86ca3690991dc6832b2270ea9e37cba34 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Wed, 7 Aug 2024 07:45:20 +0000 Subject: [PATCH 012/100] Adjust multiqc configs for updated bracken --- workflows/rnaseq/assets/multiqc/multiqc_config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml index 5d144cbdf..a2d33206a 100644 --- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml +++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml @@ -111,7 +111,7 @@ sp: fn: "*report.txt" bracken: - fn: "*bracken_species.txt" + fn: "*.kraken2.report_bracken.txt" rseqc/bam_stat: fn: "*.bam_stat.txt" From 075bca8b9fff53c017fc60d21d0e072a8cc9648c Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Wed, 7 Aug 2024 09:38:12 +0000 Subject: [PATCH 013/100] Add input validation and update scheme --- nextflow.config | 2 +- nextflow_schema.json | 39 ++++++++++++++++-- .../utils_nfcore_rnaseq_pipeline/main.nf | 41 +++++++++++++++++++ 3 files changed, 77 insertions(+), 5 deletions(-) diff --git a/nextflow.config b/nextflow.config index 5e2d8a9f2..9de4b2009 100644 --- a/nextflow.config +++ b/nextflow.config @@ -73,7 +73,7 @@ params { kallisto_quant_fraglen = 200 kallisto_quant_fraglen_sd = 200 save_merged_fastq = false - save_unaligned = true + save_unaligned = false save_align_intermeds = false skip_markduplicates = false skip_alignment = false diff --git a/nextflow_schema.json b/nextflow_schema.json index d89b6398e..fe58cca84 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -411,7 +411,7 @@ }, "min_mapped_reads": { "type": "number", - "default": 5.0, + "default": 5, "fa_icon": "fas fa-percentage", "description": "Minimum percentage of uniquely mapped reads below which samples are removed from further processing.", "help_text": "Some downstream steps in the pipeline will fail if this threshold is too low." @@ -456,14 +456,14 @@ "stranded_threshold": { "type": "number", "minimum": 0.5, - "maximum": 1.0, + "maximum": 1, "default": 0.8, "description": "The fraction of stranded reads that must be assigned to a strandedness for confident assignment. Must be at least 0.5." }, "unstranded_threshold": { "type": "number", - "minimum": 0.0, - "maximum": 1.0, + "minimum": 0, + "maximum": 1, "default": 0.1, "description": "The difference in fraction of stranded reads assigned to 'forward' and 'reverse' below which a sample is classified as 'unstranded'. By default the forward and reverse fractions must differ by less than 0.1 for the sample to be called as unstranded." } @@ -518,6 +518,18 @@ "fa_icon": "fas fa-save", "description": "Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.", "help_text": "This may either be in the form of FastQ or BAM files depending on the options available for that particular tool." + }, + "save_kraken_assignments": { + "type": "boolean", + "fa_icon": "fas fa-save", + "description": "Save read-by-read assignments from Kraken2.", + "help_text": "`--kraken_db` parameter must be provided." + }, + "save_kraken_unassigned": { + "type": "boolean", + "fa_icon": "fas fa-save", + "description": "Save reads that were not given assignment from Kraken2.", + "help_text": "`--kraken_db` parameter must be provided." } } }, @@ -539,6 +551,19 @@ "default": "bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication", "fa_icon": "fas fa-chart-pie", "description": "Specify the RSeQC modules to run." + }, + "kraken_db": { + "type": "string", + "description": "Run Kraken2 and Bracken with provided database on unaligned reads.", + "help_text": "See [pre-built Kraken/Bracken databases](https://benlangmead.github.io/aws-indexes/k2). This option must be ran with `--save_unaligned`", + "fa_icon": "fas fa-bacteria" + }, + "bracken_precision": { + "type": "string", + "default": "G", + "fa_icon": "fas fa-tree", + "description": "Taxonomic level for Bracken abundance estimations.", + "help_text": "Options are D, P, C, O, F, G, S." } } }, @@ -637,6 +662,12 @@ "fa_icon": "fas fa-fast-forward", "description": "Skip DESeq2 PCA and heatmap plotting." }, + "skip_bracken": { + "type": "boolean", + "description": "Skip Bracken.", + "fa_icon": "fas fa-fast-forward", + "help_text": "If running Kraken2, skips Bracken post-processing." + }, "skip_multiqc": { "type": "boolean", "description": "Skip MultiQC.", diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf index 8022a5c1b..989bc8f5c 100644 --- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf @@ -256,6 +256,27 @@ def validateInputParameters() { } } + // Check that unaligned reads are saved when using Kraken2 + if (params.kraken_db) { + if (!params.save_unaligned) { + error("Please provide --save_unaligned when using Kraken2 to save unaligned reads for analysis.") + } + + if (params.aligner = 'star_rsem') { + error("Kraken2 cannot be used with --aligner star_rsem since unaligned reads are not saved. Please use --aligner star_salmon or --aligner hisat2.") + } + } + + // Check that Bracken skipped option is not given when not running kraken + if (!params.kraken_db && params.skip_bracken) { + skipBrackenWithoutKrackenWarn() + } + + // Check that no kraken options are given when not running kraken + if (!params.kraken_db && (params.save_kraken_assignments || params.save_kraken_unassigned)) { + krakenArgumentsWithoutKrakenDBWarn() + } + // Check which RSeQC modules we are running def valid_rseqc_modules = ['bam_stat', 'inner_distance', 'infer_experiment', 'junction_annotation', 'junction_saturation', 'read_distribution', 'read_duplication', 'tin'] def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').collect{ it.trim().toLowerCase() } : [] @@ -471,6 +492,26 @@ def additionaFastaIndexWarn(index) { "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" } +// +// Print a warning if using '--skip_bracken' without '--kraken_db' +// +def skipBrackenWithoutKrackenWarn() { + log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " '--skip_bracken' parameter has been provided without '--kraken_db'.\n" + + " Neither bracken or kraken will run.\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" +} + +// +// Print a warning if save_kraken_assignments or save_kraken_unassigned is provided without kraken_db +// +def krakenArgumentsWithoutKrakenDBWarn() { + log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " '--save_kraken_assignments' or '--save_kraken_unassigned' parameters have been provided without '--kraken_db'.\n" + + " Kraken2 is not being run so neither will be saved.\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" +} + // // Function to generate an error if contigs in genome fasta file > 512 Mbp // From a0a225c565fb490bb92ee04c1dca5de45ba6b606 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Wed, 7 Aug 2024 12:27:46 +0000 Subject: [PATCH 014/100] Change default Bracken precision to species --- nextflow.config | 2 +- nextflow_schema.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index 9de4b2009..33cb94f49 100644 --- a/nextflow.config +++ b/nextflow.config @@ -93,7 +93,7 @@ params { skip_bracken = false save_kraken_assignments = false save_kraken_unassigned = false - bracken_precision = "G" + bracken_precision = "S" skip_rseqc = false skip_biotype_qc = false skip_deseq2_qc = false diff --git a/nextflow_schema.json b/nextflow_schema.json index fe58cca84..436f4c4ad 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -560,7 +560,7 @@ }, "bracken_precision": { "type": "string", - "default": "G", + "default": "S", "fa_icon": "fas fa-tree", "description": "Taxonomic level for Bracken abundance estimations.", "help_text": "Options are D, P, C, O, F, G, S." From bd4ea1caa77ce9e24f96c62092920392093a90f4 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Wed, 7 Aug 2024 12:28:04 +0000 Subject: [PATCH 015/100] Debug input validation --- .../utils_nfcore_rnaseq_pipeline/main.nf | 36 +++++++++++++------ 1 file changed, 26 insertions(+), 10 deletions(-) diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf index 989bc8f5c..3f5765272 100644 --- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf @@ -262,19 +262,25 @@ def validateInputParameters() { error("Please provide --save_unaligned when using Kraken2 to save unaligned reads for analysis.") } - if (params.aligner = 'star_rsem') { + if (params.aligner == 'star_rsem') { error("Kraken2 cannot be used with --aligner star_rsem since unaligned reads are not saved. Please use --aligner star_salmon or --aligner hisat2.") } } - // Check that Bracken skipped option is not given when not running kraken - if (!params.kraken_db && params.skip_bracken) { - skipBrackenWithoutKrackenWarn() - } + //Check that Kraken/Bracken parameters are not provided without the --kraken_db + if (!params.kraken_db) { + + if (!params.bracken_precision.equals('S')) { + brackenPrecisionWithoutKrakenDBWarn() + } + + if (params.skip_bracken) { + skipBrackenWithoutKrackenWarn() + } - // Check that no kraken options are given when not running kraken - if (!params.kraken_db && (params.save_kraken_assignments || params.save_kraken_unassigned)) { - krakenArgumentsWithoutKrakenDBWarn() + if (params.save_kraken_assignments || params.save_kraken_unassigned) { + krakenArgumentsWithoutKrakenDBWarn() + } } // Check which RSeQC modules we are running @@ -498,12 +504,12 @@ def additionaFastaIndexWarn(index) { def skipBrackenWithoutKrackenWarn() { log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " '--skip_bracken' parameter has been provided without '--kraken_db'.\n" + - " Neither bracken or kraken will run.\n" + + " Neither Bracken nor Kraken2 will run.\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" } // -// Print a warning if save_kraken_assignments or save_kraken_unassigned is provided without kraken_db +// Print a warning if --save_kraken_assignments or --save_kraken_unassigned is provided without --kraken_db // def krakenArgumentsWithoutKrakenDBWarn() { log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + @@ -512,6 +518,16 @@ def krakenArgumentsWithoutKrakenDBWarn() { "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" } +/// +/// Print a warning if --bracken-precision is provided without --kraken_db +/// +def brackenPrecisionWithoutKrakenDBWarn() { + log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " '--bracken-precision' parameter has been provided without '--kraken_db'.\n" + + " Bracken will not run so precision will not be set.\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" +} + // // Function to generate an error if contigs in genome fasta file > 512 Mbp // From 77898275bed7e0a8ae48084e0aed763a77da4ed8 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Wed, 7 Aug 2024 12:28:44 +0000 Subject: [PATCH 016/100] Documentation/output image --- README.md | 1 + docs/images/bracken-top-n-plot.png | Bin 0 -> 55992 bytes docs/output.md | 23 ++++++++++++++++++++++- 3 files changed, 23 insertions(+), 1 deletion(-) create mode 100644 docs/images/bracken-top-n-plot.png diff --git a/README.md b/README.md index 411dfd3f4..15fe29d97 100644 --- a/README.md +++ b/README.md @@ -44,6 +44,7 @@ 3. [`dupRadar`](https://bioconductor.org/packages/release/bioc/html/dupRadar.html) 4. [`Preseq`](http://smithlabresearch.org/software/preseq/) 5. [`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html) + 6. [`Kraken2`](https://ccb.jhu.edu/software/kraken2/) -> [`Bracken`](https://ccb.jhu.edu/software/bracken/) on unaligned sequences; _optional_ 15. Pseudoalignment and quantification ([`Salmon`](https://combine-lab.github.io/salmon/) or ['Kallisto'](https://pachterlab.github.io/kallisto/); _optional_) 16. Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks ([`MultiQC`](http://multiqc.info/), [`R`](https://www.r-project.org/)) diff --git a/docs/images/bracken-top-n-plot.png b/docs/images/bracken-top-n-plot.png new file mode 100644 index 0000000000000000000000000000000000000000..ac2d485f67e90c389be6f169b0ff79dbae36f67e GIT binary patch literal 55992 zcmeFacT|*HvnCD*h$u!76=+aIkRT#CBOD}25@|9tlCwyX3?@v_0+N%6B*{4kQ9+a@ zH%L~AO;ndCEj1e6|J(l~2E3(voL;d66=?9Q}BCKjKA_EkVMb?$3${%IoSHY9# zzq4(*gcBCNOG$I9#Bf@+o-5FQYm|AyU}PgwM^G!94=cT0uIJuofvXSP^Yz!YU$~Nz zWp^r_JPfb;Q2omj-r9@E#F>60Zmbl2ReRVp)*Ozz!r;&y-LGerU=gW%Kh^lnoR9%+4JK@NynNYZ z0`ML^hWp_0sL)?Nuwn()M*RIht@D(Bxnr4`8hOdUu_AT-qfYJ7dwWRHOG1vNeU=kl z>e4)eW;vEsKN=bKW8ac&Q~7MKPfkSDZKZlHcPQWnUD_OSs~10_-rKpgDX}M*Oa1(E zH!{4_cWGc`yXPsRXlK$R4?V(tdSmOx5GFh65_q<_aCNDQPe)#h8xhw(nQY(K^k_V3 z6}>(Ymsk0O?-DW>GOjSs9VPMmSYgJ;_q$T(cj^q@d`p81+>6rnJK`&Gh7|4cokr+$ 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zUE?(P7u4}vIKOm)Eg@;2AWIs81`(2}>NXhq=x_#|xq!1AKyit&|DX zLM&H%PP8k!CEG`yVSn@Ry3bymD_C90S3mY=^wp+-2y~vx{@4UAkFvkqZ22dxaTinK zlHfh2H2;^dvzaVuibW)vrcl}q${`egiHZGedSG|nPM5R) E3$MultiQC - DESeq2 sample similarity plot

+### Kraken2/Bracken + +
+Output files + +- `kraken2/kraken_reports` + - `*.kraken2.report.txt`: Classification of unaligned reads in the Kraken report format. See the [kraken2 manual](https://github.com/DerrickWood/kraken2/wiki/Manual#output-formats) for more details + - `*.classified*.fastq.gz` If `--save_kraken_alignments`, outputs fastq file for each sample with each classified read annotated with taxonomic identification from Kraken2. + - `*.unclassified*.fastq.gz` If `save_kraken_unassigned`, outputs fastq file with all reads that were not classified by Kraken2. +- `bracken/` + - `*.kraken2.report_bracken.txt`: Kraken-style reports of the Bracken abundance estimate results. See the [kraken2 manual](https://github.com/DerrickWood/kraken2/wiki/Manual#output-formats) for more details. + - `*.tsv` Summary of estimated reads for each taxon member at the given classification level and what corrections were made from Kraken2. + +
+ +[Kraken2](https://ccb.jhu.edu/software/kraken2/) is a taxonomic classification tool that uses k-mer matches paired with a lowest common ancestory (LCA) algorithm to classify species reads. [Bracken](https://ccb.jhu.edu/software/bracken/) is a statistical method to generate abundance estimates based off of the Kraken2 output. These algorithms are run on unaligned sequences to detect potential contamination of samples. MultiQC reports the top 5 taxon members detected at the level of classification used for Bracken, with toggles available for higher taxonomic levels. If Bracken is skipped, MultiQC will report the top 5 species detected by Kraken2. + +![MultiQC - Bracken top species plot](images/bracken-top-n-plot.png) + + ### MultiQC
@@ -673,7 +694,7 @@ Results generated by MultiQC collate pipeline QC from supported tools i.e. FastQ ### Pseudoalignment -The principal output files are the same between Salmon and Kallsto: +The principal output files are the same between Salmon and Kallisto:
Output files From 336a7b02c8f75d0347f946901c85a1fd6e459ac5 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Wed, 7 Aug 2024 16:16:38 +0300 Subject: [PATCH 017/100] Update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e62628fc6..801b577e8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,7 +22,7 @@ Special thanks to the following for their contributions to the release: Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. ### Enhancements & fixes - +- [PR #1351](https://github.com/nf-core/rnaseq/pull/1351) - Adding Kraken2/Bracken on unaligned reads as an additional quality control step to detect sample contamination - [PR #1186](https://github.com/nf-core/rnaseq/pull/1186) - Properly update qualimap/rnaseq module (ie not patch) - [PR #1197](https://github.com/nf-core/rnaseq/pull/1197) - Delete lib directory and replace with utils\_\* subworkflows - [PR #1199](https://github.com/nf-core/rnaseq/pull/1199) - Replace modules.config with more modular config files per module/subworkflow/workflow From a1e1d99d185f6fdd408b23a36a777dcb51ecb3e7 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Fri, 9 Aug 2024 10:40:22 +0300 Subject: [PATCH 018/100] Update Kraken2 module --- modules.json | 2 +- modules/nf-core/kraken2/kraken2/tests/main.nf.test | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/modules.json b/modules.json index 20b52c3a1..089f9f21e 100644 --- a/modules.json +++ b/modules.json @@ -97,7 +97,7 @@ }, "kraken2/kraken2": { "branch": "master", - "git_sha": "ca87ad032a62f025f0c373facacef2df0c5411b2", + "git_sha": "a13d5d945742a60bbef6e5c177e81cda540f75dc", "installed_by": ["modules"] }, "multiqc": { diff --git a/modules/nf-core/kraken2/kraken2/tests/main.nf.test b/modules/nf-core/kraken2/kraken2/tests/main.nf.test index 4c5130217..c0843df29 100644 --- a/modules/nf-core/kraken2/kraken2/tests/main.nf.test +++ b/modules/nf-core/kraken2/kraken2/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { input[0] = Channel.of([ [], file( - params.test_data['sarscov2']['genome']['kraken2_tar_gz'], + params.modules_testdata_base_path + "genomics/sarscov2/genome/db/kraken2.tar.gz", checkIfExists: true ) ]) @@ -32,7 +32,7 @@ nextflow_process { input[0] = [ [ id:'test', single_end:true ], // meta map [ file( - params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], + params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true )] ] @@ -69,16 +69,16 @@ nextflow_process { [ id:'test', single_end:false ], // meta map [ file( - params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], + params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true ), file( - params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], + params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true ) + ] ] - ] input[1] = UNTAR.out.untar.map{ it[1] } input[2] = true input[3] = false @@ -117,7 +117,7 @@ nextflow_process { input[0] = [ [ id:'test', single_end:true ], // meta map [ file( - params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], + params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true )] ] From 33c94836fba117a612b569ab1c5e2f64ebe5846c Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Fri, 9 Aug 2024 12:59:23 +0300 Subject: [PATCH 019/100] Linting --- CHANGELOG.md | 1 + docs/output.md | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 801b577e8..f571b434a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,7 @@ Special thanks to the following for their contributions to the release: Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. ### Enhancements & fixes + - [PR #1351](https://github.com/nf-core/rnaseq/pull/1351) - Adding Kraken2/Bracken on unaligned reads as an additional quality control step to detect sample contamination - [PR #1186](https://github.com/nf-core/rnaseq/pull/1186) - Properly update qualimap/rnaseq module (ie not patch) - [PR #1197](https://github.com/nf-core/rnaseq/pull/1197) - Delete lib directory and replace with utils\_\* subworkflows diff --git a/docs/output.md b/docs/output.md index 9a6b73ef8..144caabd5 100644 --- a/docs/output.md +++ b/docs/output.md @@ -674,7 +674,6 @@ The plot on the left hand side shows the standard PC plot - notice the variable ![MultiQC - Bracken top species plot](images/bracken-top-n-plot.png) - ### MultiQC
From 102152e5b07b1fa9d7f65c913e388db9bc6bc2c4 Mon Sep 17 00:00:00 2001 From: Ezra Greenberg Date: Thu, 15 Aug 2024 16:32:32 +0000 Subject: [PATCH 020/100] Change to --contaminant_screening param --- .../nf-core/bracken/bracken/nextflow.config | 2 +- .../nf-core/kraken2/kraken2/nextflow.config | 2 +- nextflow.config | 2 +- nextflow_schema.json | 20 +++++----- .../utils_nfcore_rnaseq_pipeline/main.nf | 39 +++++++------------ workflows/rnaseq/main.nf | 9 ++--- 6 files changed, 29 insertions(+), 45 deletions(-) diff --git a/modules/nf-core/bracken/bracken/nextflow.config b/modules/nf-core/bracken/bracken/nextflow.config index e6d396652..052a75482 100644 --- a/modules/nf-core/bracken/bracken/nextflow.config +++ b/modules/nf-core/bracken/bracken/nextflow.config @@ -1,5 +1,5 @@ if (!params.skip_alignment && !params.skip_qc) { - if (params.kraken_db && !params.skip_bracken) { + if (params.contaminant_screening == 'kraken2_bracken') { process { withName: 'BRACKEN' { ext.args = "-l ${params.bracken_precision}" diff --git a/modules/nf-core/kraken2/kraken2/nextflow.config b/modules/nf-core/kraken2/kraken2/nextflow.config index 0070ad9fd..f4375210f 100644 --- a/modules/nf-core/kraken2/kraken2/nextflow.config +++ b/modules/nf-core/kraken2/kraken2/nextflow.config @@ -1,5 +1,5 @@ if (!params.skip_alignment && !params.skip_qc) { - if (params.kraken_db) { + if (params.contaminant_screening in ['kraken2', 'kraken2_bracken']) { process { withName: 'KRAKEN2' { ext.args = "--confidence 0.05 --minimum-hit-groups 3" diff --git a/nextflow.config b/nextflow.config index 33cb94f49..4a66931dd 100644 --- a/nextflow.config +++ b/nextflow.config @@ -89,8 +89,8 @@ params { skip_preseq = true skip_dupradar = false skip_qualimap = false + contaminant_screening = null kraken_db = null - skip_bracken = false save_kraken_assignments = false save_kraken_unassigned = false bracken_precision = "S" diff --git a/nextflow_schema.json b/nextflow_schema.json index 436f4c4ad..b524e762f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -552,18 +552,24 @@ "fa_icon": "fas fa-chart-pie", "description": "Specify the RSeQC modules to run." }, + "contaminant_screening": { + "type": "string", + "description": "Tool to use for detecting contaminants in unaligned reads - available options are 'kraken2' and 'kraken2_bracken'", + "fa_icon": "fas fa-virus-slash", + "enum": ["kraken2", "kraken2_bracken"] + }, "kraken_db": { "type": "string", - "description": "Run Kraken2 and Bracken with provided database on unaligned reads.", - "help_text": "See [pre-built Kraken/Bracken databases](https://benlangmead.github.io/aws-indexes/k2). This option must be ran with `--save_unaligned`", - "fa_icon": "fas fa-bacteria" + "description": "Database when using Kraken2/Bracken for contaminant screening.", + "help_text": "See [pre-built Kraken2/Bracken databases](https://benlangmead.github.io/aws-indexes/k2).", + "fa_icon": "fas fa-fish" }, "bracken_precision": { "type": "string", "default": "S", "fa_icon": "fas fa-tree", "description": "Taxonomic level for Bracken abundance estimations.", - "help_text": "Options are D, P, C, O, F, G, S." + "enum": ["D", "P", "C", "O", "F", "G", "S"] } } }, @@ -662,12 +668,6 @@ "fa_icon": "fas fa-fast-forward", "description": "Skip DESeq2 PCA and heatmap plotting." }, - "skip_bracken": { - "type": "boolean", - "description": "Skip Bracken.", - "fa_icon": "fas fa-fast-forward", - "help_text": "If running Kraken2, skips Bracken post-processing." - }, "skip_multiqc": { "type": "boolean", "description": "Skip MultiQC.", diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf index 3f5765272..0e64e4807 100644 --- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf @@ -256,28 +256,24 @@ def validateInputParameters() { } } - // Check that unaligned reads are saved when using Kraken2 - if (params.kraken_db) { - if (!params.save_unaligned) { - error("Please provide --save_unaligned when using Kraken2 to save unaligned reads for analysis.") - } - + //General checks for if contaminant screening is used + if (params.contaminant_screening) { if (params.aligner == 'star_rsem') { - error("Kraken2 cannot be used with --aligner star_rsem since unaligned reads are not saved. Please use --aligner star_salmon or --aligner hisat2.") + error("Contaminant screeneing cannot be done with --aligner star_rsem since unaligned reads are not saved. Please use --aligner star_salmon or --aligner hisat2.") } } - //Check that Kraken/Bracken parameters are not provided without the --kraken_db - if (!params.kraken_db) { - + // Check that Kraken/Bracken database provided if using kraken2/bracken + if (params.contaminant_screening in ['kraken2', 'kraken2_bracken']) { + if (!params.kraken_db) { + error("Contaminant screening set to kraken2 but not database is provided. Please provide a database with the --kraken_db option.") + } + //Check that Kraken/Bracken parameters are not provided when Kraken2 is not being used + } else { if (!params.bracken_precision.equals('S')) { brackenPrecisionWithoutKrakenDBWarn() } - if (params.skip_bracken) { - skipBrackenWithoutKrackenWarn() - } - if (params.save_kraken_assignments || params.save_kraken_unassigned) { krakenArgumentsWithoutKrakenDBWarn() } @@ -498,22 +494,13 @@ def additionaFastaIndexWarn(index) { "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" } -// -// Print a warning if using '--skip_bracken' without '--kraken_db' -// -def skipBrackenWithoutKrackenWarn() { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " '--skip_bracken' parameter has been provided without '--kraken_db'.\n" + - " Neither Bracken nor Kraken2 will run.\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" -} - // // Print a warning if --save_kraken_assignments or --save_kraken_unassigned is provided without --kraken_db // def krakenArgumentsWithoutKrakenDBWarn() { log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " '--save_kraken_assignments' or '--save_kraken_unassigned' parameters have been provided without '--kraken_db'.\n" + + " '--save_kraken_assignments' or '--save_kraken_unassigned' parameters\n" + + " have been provided when contaminant screening is not set to Kraken2.\n" + " Kraken2 is not being run so neither will be saved.\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" } @@ -523,7 +510,7 @@ def krakenArgumentsWithoutKrakenDBWarn() { /// def brackenPrecisionWithoutKrakenDBWarn() { log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " '--bracken-precision' parameter has been provided without '--kraken_db'.\n" + + " '--bracken-precision' parameter has been provided without Kraken2 contaminant screening.\n" + " Bracken will not run so precision will not be set.\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" } diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index 323db5d02..1100dfbbf 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -640,7 +640,7 @@ workflow RNASEQ { ch_multiqc_files = ch_multiqc_files.mix(ch_fail_strand_multiqc.collectFile(name: 'fail_strand_check_mqc.tsv')) } - if (params.kraken_db) { + if (params.contaminant_screening in ['kraken2', 'kraken2_bracken'] ) { KRAKEN2 ( ch_unaligned_sequences, params.kraken_db, @@ -650,12 +650,9 @@ workflow RNASEQ { ch_kraken_reports = KRAKEN2.out.report ch_versions = ch_versions.mix(KRAKEN2.out.versions) - // Only put Kraken2 output in MultiQC if Bracken is not run - if (params.skip_bracken) { + if (params.contaminant_screening == 'kraken2') { ch_multiqc_files = ch_multiqc_files.mix(KRAKEN2.out.report.collect{it[1]}) - } - - if (!params.skip_bracken) { + } else if (params.contaminant_screening == 'kraken2_bracken') BRACKEN ( ch_kraken_reports, params.kraken_db From 6dd752109e68ebb142bccc48a822593ad37743f4 Mon Sep 17 00:00:00 2001 From: Ezra Greenberg Date: Thu, 15 Aug 2024 19:27:03 +0000 Subject: [PATCH 021/100] Fixing save unaligned default --- modules.json | 3 +- .../nf-core/hisat2/align/hisat2-align.diff | 56 +++++++++++++++++++ modules/nf-core/hisat2/align/main.nf | 6 +- subworkflows/local/align_star/nextflow.config | 2 +- 4 files changed, 62 insertions(+), 5 deletions(-) create mode 100644 modules/nf-core/hisat2/align/hisat2-align.diff diff --git a/modules.json b/modules.json index 089f9f21e..c84770ba7 100644 --- a/modules.json +++ b/modules.json @@ -73,7 +73,8 @@ "hisat2/align": { "branch": "master", "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f", - "installed_by": ["fastq_align_hisat2"] + "installed_by": ["fastq_align_hisat2"], + "patch": "modules/nf-core/hisat2/align/hisat2-align.diff" }, "hisat2/build": { "branch": "master", diff --git a/modules/nf-core/hisat2/align/hisat2-align.diff b/modules/nf-core/hisat2/align/hisat2-align.diff new file mode 100644 index 000000000..6086520f6 --- /dev/null +++ b/modules/nf-core/hisat2/align/hisat2-align.diff @@ -0,0 +1,56 @@ +Changes in module 'nf-core/hisat2/align' +--- modules/nf-core/hisat2/align/main.nf ++++ modules/nf-core/hisat2/align/main.nf +@@ -36,7 +36,7 @@ + ss = "$splicesites" ? "--known-splicesite-infile $splicesites" : '' + def seq_center = params.seq_center ? "--rg-id ${prefix} --rg SM:$prefix --rg CN:${params.seq_center.replaceAll('\\s','_')}" : "--rg-id ${prefix} --rg SM:$prefix" + if (meta.single_end) { +- def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' ++ def unaligned = params.save_unaligned || params.contaminant_screening ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' + """ + INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'` + hisat2 \\ +@@ -58,7 +58,7 @@ + END_VERSIONS + """ + } else { +- def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' ++ def unaligned = params.save_unaligned || params.contaminant_screening ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' + """ + INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'` + hisat2 \\ +@@ -93,7 +93,7 @@ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" +- def unaligned = params.save_unaligned ? "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz \n echo '' | gzip > ${prefix}.unmapped_2.fastq.gz" : '' ++ def unaligned = params.save_unaligned || params.contaminant_screening ? "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz \n echo '' | gzip > ${prefix}.unmapped_2.fastq.gz" : '' + def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + """ + ${unaligned} + +--- modules/nf-core/hisat2/align/tests/main.nf.test ++++ modules/nf-core/hisat2/align/tests/main.nf.test +@@ -3,12 +3,6 @@ + name "Test Process HISAT2_ALIGN" + script "../main.nf" + process "HISAT2_ALIGN" +- tag "modules" +- tag "modules_nfcore" +- tag "hisat2" +- tag "hisat2/align" +- tag "hisat2/build" +- tag "hisat2/extractsplicesites" + + test("Single-End") { + + +--- modules/nf-core/hisat2/align/tests/tags.yml ++++ /dev/null +@@ -1,4 +0,0 @@ +-hisat2/align: +- - modules/nf-core/hisat2/align/** +- - modules/nf-core/hisat2/build/** +- - modules/nf-core/hisat2/extractsplicesites/** + +************************************************************ diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index ea186f62a..a8d1880c5 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -36,7 +36,7 @@ process HISAT2_ALIGN { ss = "$splicesites" ? "--known-splicesite-infile $splicesites" : '' def seq_center = params.seq_center ? "--rg-id ${prefix} --rg SM:$prefix --rg CN:${params.seq_center.replaceAll('\\s','_')}" : "--rg-id ${prefix} --rg SM:$prefix" if (meta.single_end) { - def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' + def unaligned = params.save_unaligned || params.contaminant_screening ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' """ INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'` hisat2 \\ @@ -58,7 +58,7 @@ process HISAT2_ALIGN { END_VERSIONS """ } else { - def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' + def unaligned = params.save_unaligned || params.contaminant_screening ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' """ INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'` hisat2 \\ @@ -93,7 +93,7 @@ process HISAT2_ALIGN { stub: def prefix = task.ext.prefix ?: "${meta.id}" - def unaligned = params.save_unaligned ? "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz \n echo '' | gzip > ${prefix}.unmapped_2.fastq.gz" : '' + def unaligned = params.save_unaligned || params.contaminant_screening ? "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz \n echo '' | gzip > ${prefix}.unmapped_2.fastq.gz" : '' def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ ${unaligned} diff --git a/subworkflows/local/align_star/nextflow.config b/subworkflows/local/align_star/nextflow.config index 119eb6e4a..511ff6e63 100644 --- a/subworkflows/local/align_star/nextflow.config +++ b/subworkflows/local/align_star/nextflow.config @@ -22,7 +22,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') { --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend --outSAMstrandField intronMotif - ${params.save_unaligned ? '--outReadsUnmapped Fastx' : ''} + ${params.save_unaligned || params.contaminant_screening ? '--outReadsUnmapped Fastx' : ''} """.trim()) // Consolidate the extra arguments From fdd85ad0926f0bb78ea87d0ce61a731ae3b90fe3 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Thu, 15 Aug 2024 17:53:51 -0400 Subject: [PATCH 022/100] Debugging --- subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf | 7 +++---- workflows/rnaseq/main.nf | 2 +- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf index 0e64e4807..2b556516c 100644 --- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf @@ -274,7 +274,7 @@ def validateInputParameters() { brackenPrecisionWithoutKrakenDBWarn() } - if (params.save_kraken_assignments || params.save_kraken_unassigned) { + if (params.save_kraken_assignments || params.save_kraken_unassigned || params.kraken_db) { krakenArgumentsWithoutKrakenDBWarn() } } @@ -499,9 +499,8 @@ def additionaFastaIndexWarn(index) { // def krakenArgumentsWithoutKrakenDBWarn() { log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " '--save_kraken_assignments' or '--save_kraken_unassigned' parameters\n" + - " have been provided when contaminant screening is not set to Kraken2.\n" + - " Kraken2 is not being run so neither will be saved.\n" + + " 'Kraken2 related arguments have been provided without setting contaminant\n" + + " screening to Kraken2. Kraken2 is not being run so these will not be used.\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" } diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index 1100dfbbf..a6725ec7f 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -652,7 +652,7 @@ workflow RNASEQ { if (params.contaminant_screening == 'kraken2') { ch_multiqc_files = ch_multiqc_files.mix(KRAKEN2.out.report.collect{it[1]}) - } else if (params.contaminant_screening == 'kraken2_bracken') + } else if (params.contaminant_screening == 'kraken2_bracken') { BRACKEN ( ch_kraken_reports, params.kraken_db From c0099d4a36980bb994651d203c4846f7776c9832 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Thu, 15 Aug 2024 17:55:14 -0400 Subject: [PATCH 023/100] Update usage --- docs/usage.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/usage.md b/docs/usage.md index b613ab79d..cbf752a89 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -296,6 +296,10 @@ Notes: By default, the input GTF file will be filtered to ensure that sequence names correspond to those in the genome fasta file, and to remove rows with empty transcript identifiers. Filtering can be bypassed completely where you are confident it is not necessary, using the `--skip_gtf_filter` parameter. If you just want to skip the 'transcript_id' checking component of the GTF filtering script used in the pipeline this can be disabled specifically using the `--skip_gtf_transcript_filter` parameter. +## Contamination screening options + +The pipeline provides the option to scan unaligned reads for contamination from other species by using [Kraken2](https://ccb.jhu.edu/software/kraken2/) with or without corrections from [Bracken](https://ccb.jhu.edu/software/bracken/). As Bracken is not a particularly expensive algorithm, we recommend using it to correct the abundance estimations from Kraken. An important note is that Kraken2 is [sensitive to the database](https://doi.org/10.1099/mgen.0.000949) that it is used with. It is [particularly important](https://doi.org/10.1128/mbio.01607-23) to ensure that the host genome is part of the database, and if you are particularly concerned about specific contaminants, it may be worthwhile to use a smaller database that contains primarily those contaminants rather than the full standard database. Various pre-built databases can be found [here](https://benlangmead.github.io/aws-indexes/k2) and instructions for building a custom database can be found at the [Kraken2 documentation](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown). Genomes of contaminants detected in previous sequencing experiments can be found on the [OpenContami website](https://openlooper.hgc.jp/opencontami/help/help_oct.php). Additionally, note that while one of the primary strengths of Kraken2 is that it can detect loaw abundance contaminants in a sample, false positives can also occur. If a very low number of reads of some contaminating species is detected, these results should be treated with caution. + ## Running the pipeline The typical command for running the pipeline is as follows: From c25aa50f58f39e13b863420dd63afef68d0893c3 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Thu, 15 Aug 2024 17:55:30 -0400 Subject: [PATCH 024/100] Provide motivation for Kraken2 parameters --- modules/nf-core/kraken2/kraken2/nextflow.config | 2 ++ 1 file changed, 2 insertions(+) diff --git a/modules/nf-core/kraken2/kraken2/nextflow.config b/modules/nf-core/kraken2/kraken2/nextflow.config index f4375210f..421b2a1e0 100644 --- a/modules/nf-core/kraken2/kraken2/nextflow.config +++ b/modules/nf-core/kraken2/kraken2/nextflow.config @@ -2,6 +2,8 @@ if (!params.skip_alignment && !params.skip_qc) { if (params.contaminant_screening in ['kraken2', 'kraken2_bracken']) { process { withName: 'KRAKEN2' { + // See https://doi.org/10.1080/19490976.2024.2323235 for the confidence level + // and https://doi.org/10.1038/s41596-022-00738-y for the minimum-hit-groups ext.args = "--confidence 0.05 --minimum-hit-groups 3" publishDir = [ path: { "${params.outdir}/kraken2/kraken_reports" }, From 0063c2df38deeee0c7e0bf96ec50455f696ea94e Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Fri, 16 Aug 2024 13:23:14 -0400 Subject: [PATCH 025/100] Fix typo --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index cbf752a89..a86387066 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -298,7 +298,7 @@ By default, the input GTF file will be filtered to ensure that sequence names co ## Contamination screening options -The pipeline provides the option to scan unaligned reads for contamination from other species by using [Kraken2](https://ccb.jhu.edu/software/kraken2/) with or without corrections from [Bracken](https://ccb.jhu.edu/software/bracken/). As Bracken is not a particularly expensive algorithm, we recommend using it to correct the abundance estimations from Kraken. An important note is that Kraken2 is [sensitive to the database](https://doi.org/10.1099/mgen.0.000949) that it is used with. It is [particularly important](https://doi.org/10.1128/mbio.01607-23) to ensure that the host genome is part of the database, and if you are particularly concerned about specific contaminants, it may be worthwhile to use a smaller database that contains primarily those contaminants rather than the full standard database. Various pre-built databases can be found [here](https://benlangmead.github.io/aws-indexes/k2) and instructions for building a custom database can be found at the [Kraken2 documentation](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown). Genomes of contaminants detected in previous sequencing experiments can be found on the [OpenContami website](https://openlooper.hgc.jp/opencontami/help/help_oct.php). Additionally, note that while one of the primary strengths of Kraken2 is that it can detect loaw abundance contaminants in a sample, false positives can also occur. If a very low number of reads of some contaminating species is detected, these results should be treated with caution. +The pipeline provides the option to scan unaligned reads for contamination from other species by using [Kraken2](https://ccb.jhu.edu/software/kraken2/) with or without corrections from [Bracken](https://ccb.jhu.edu/software/bracken/). As Bracken is not a particularly expensive algorithm, we recommend using it to correct the abundance estimations from Kraken. An important note is that Kraken2 is [sensitive to the database](https://doi.org/10.1099/mgen.0.000949) that it is used with. It is [particularly important](https://doi.org/10.1128/mbio.01607-23) to ensure that the host genome is part of the database, and if you are particularly concerned about specific contaminants, it may be worthwhile to use a smaller database that contains primarily those contaminants rather than the full standard database. Various pre-built databases can be found [here](https://benlangmead.github.io/aws-indexes/k2) and instructions for building a custom database can be found at the [Kraken2 documentation](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown). Genomes of contaminants detected in previous sequencing experiments can be found on the [OpenContami website](https://openlooper.hgc.jp/opencontami/help/help_oct.php). Additionally, note that while one of the primary strengths of Kraken2 is that it can detect low abundance contaminants in a sample, false positives can also occur. 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Output files -- `kraken2/kraken_reports` +- `/contaminants/kraken2/kraken_reports` - `*.kraken2.report.txt`: Classification of unaligned reads in the Kraken report format. See the [kraken2 manual](https://github.com/DerrickWood/kraken2/wiki/Manual#output-formats) for more details - `*.classified*.fastq.gz` If `--save_kraken_alignments`, outputs fastq file for each sample with each classified read annotated with taxonomic identification from Kraken2. - `*.unclassified*.fastq.gz` If `save_kraken_unassigned`, outputs fastq file with all reads that were not classified by Kraken2. -- `bracken/` +- `/contaminants/bracken/` - `*.kraken2.report_bracken.txt`: Kraken-style reports of the Bracken abundance estimate results. See the [kraken2 manual](https://github.com/DerrickWood/kraken2/wiki/Manual#output-formats) for more details. - `*.tsv` Summary of estimated reads for each taxon member at the given classification level and what corrections were made from Kraken2. diff --git a/modules/nf-core/bracken/bracken/nextflow.config b/modules/nf-core/bracken/bracken/nextflow.config index 052a75482..975a9793a 100644 --- a/modules/nf-core/bracken/bracken/nextflow.config +++ b/modules/nf-core/bracken/bracken/nextflow.config @@ -4,7 +4,7 @@ if (!params.skip_alignment && !params.skip_qc) { withName: 'BRACKEN' { ext.args = "-l ${params.bracken_precision}" publishDir = [ - path: { "${params.outdir}/bracken" }, + path: { "${params.outdir}/${params.aligner}/contaminants/bracken" }, mode: params.publish_dir_mode ] } diff --git a/modules/nf-core/kraken2/kraken2/nextflow.config b/modules/nf-core/kraken2/kraken2/nextflow.config index 421b2a1e0..7289bd9a1 100644 --- a/modules/nf-core/kraken2/kraken2/nextflow.config +++ b/modules/nf-core/kraken2/kraken2/nextflow.config @@ -6,7 +6,7 @@ if (!params.skip_alignment && !params.skip_qc) { // and https://doi.org/10.1038/s41596-022-00738-y for the minimum-hit-groups ext.args = "--confidence 0.05 --minimum-hit-groups 3" publishDir = [ - path: { "${params.outdir}/kraken2/kraken_reports" }, + path: { "${params.outdir}/${params.aligner}/contaminants/kraken2/kraken_reports" }, mode: params.publish_dir_mode ] } From 7b6915c40c73e309368cc9bf16f1a6b190da4401 Mon Sep 17 00:00:00 2001 From: Paolo Di Tommaso Date: Fri, 6 Sep 2024 15:37:24 +0200 Subject: [PATCH 030/100] Update main.nf --- workflows/rnaseq/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index 0b702e641..e5756d393 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -611,7 +611,7 @@ workflow RNASEQ { ch_strand_comparison = BAM_RSEQC.out.inferexperiment_txt .map { meta, strand_log -> - def rseqc_inferred_strand = getInferexperimentStrandedness(strand_log, stranded_threshold = params.stranded_threshold, unstranded_threshold = params.unstranded_threshold) + def rseqc_inferred_strand = getInferexperimentStrandedness(strand_log, params.stranded_threshold, params.unstranded_threshold) rseqc_strandedness = rseqc_inferred_strand.inferred_strandedness def status = 'fail' From 69f2d0a847ea9a8cba5e5483133ea9e55a6073ca Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Tue, 10 Sep 2024 10:18:13 -0400 Subject: [PATCH 031/100] Update Changelog --- CHANGELOG.md | 63 ++++++++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 59 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 061a10cb6..0dbb374c5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,44 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v3.15.0dev - [date] +## v3.16.0dev - [date] + +Special thanks to the following for their contributions to the release: + +Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. + +### Enhancements & fixes + +- [PR #1351](https://github.com/nf-core/rnaseq/pull/1351) - Adding Kraken2/Bracken on unaligned reads as an additional quality control step to detect sample contamination + +### Parameters +| Old parameter | New parameter | +| ------------------ | `--contaminant_screening` | +| | `--kraken_db` | +| | `--save_kraken_assignments` | +| | `--save_kraken_unassigned` | +| | `--bracken_precision` | + +> **NB:** Parameter has been **updated** if both old and new parameter information is present. +> **NB:** Parameter has been **added** if just the new parameter information is present. +> **NB:** Parameter has been **removed** if new parameter information isn't present. + +### Software dependencies + +| Dependency | Old version | New version | +| -------------- | ----------- | ----------- | +| `Kraken2` | ----------- | 2.1.3 | +| `Bracken` | ----------- | 2.9 | + +> **NB:** Dependency has been **updated** if both old and new version information is present. +> +> **NB:** Dependency has been **added** if just the new version information is present. +> +> **NB:** Dependency has been **removed** if new version information isn't present. + +### Credits + +## [[3.15.0](https://github.com/nf-core/rnaseq/releases/tag/3.15.0)] - 2024-09-04 ### Credits @@ -17,6 +54,7 @@ Special thanks to the following for their contributions to the release: - [Luke Zappia](https://github.com/lazappi) - [Matthias Zepper](https://github.com/MatthiasZepper) - [Maxime Garcia](https://github.com/maxulysse) +- [Pieter Moris](https://github.com/pmoris) - [Rob Syme](https://github.com/robsyme) - [Thomas Danhorn](https://github.com/tdanhorn) @@ -24,7 +62,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements ### Enhancements & fixes -- [PR #1351](https://github.com/nf-core/rnaseq/pull/1351) - Adding Kraken2/Bracken on unaligned reads as an additional quality control step to detect sample contamination +- [PR #1180](https://github.com/nf-core/rnaseq/pull/1180) - Bump pipeline version to 3.15.0dev - [PR #1186](https://github.com/nf-core/rnaseq/pull/1186) - Properly update qualimap/rnaseq module (ie not patch) - [PR #1197](https://github.com/nf-core/rnaseq/pull/1197) - Delete lib directory and replace with utils\_\* subworkflows - [PR #1199](https://github.com/nf-core/rnaseq/pull/1199) - Replace modules.config with more modular config files per module/subworkflow/workflow @@ -75,7 +113,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1272](https://github.com/nf-core/rnaseq/pull/1272) - Simple pipeline level nf-tests - [PR #1274](https://github.com/nf-core/rnaseq/pull/1274) - Update bam_markduplicates_picard subworkflow - [PR #1278](https://github.com/nf-core/rnaseq/pull/1278) - Delocalise pseudo quant workflow -- [PR #1279](https://github.com/nf-core/rnaseq/pull/1279) - Add psueudoaligner pipeline level tests to test suite +- [PR #1279](https://github.com/nf-core/rnaseq/pull/1279) - Add pseudoaligner pipeline level tests to test suite - [PR #1280](https://github.com/nf-core/rnaseq/pull/1280) - Reorganise pipeline level tests into flat directory structure - [PR #1282](https://github.com/nf-core/rnaseq/pull/1282) - Fix CHANGELOG error - [PR #1283](https://github.com/nf-core/rnaseq/pull/1283) - Add output files to nf-test snapshot @@ -103,13 +141,29 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1330](https://github.com/nf-core/rnaseq/pull/1330) - Update all nf-core/modules and subworkflows - [PR #1331](https://github.com/nf-core/rnaseq/pull/1331) - Adding stubs for local modules - [PR #1334](https://github.com/nf-core/rnaseq/pull/1334) - Update all nf-core/modules and subworkflows with stubs -- [PR #1336](https://github.com/nf-core/rnaseq/pull/1334) - Use nf-core/setup-nf-test to install nf-test from cache during CI/CD +- [PR #1335](https://github.com/nf-core/rnaseq/pull/1335) - Adding stubs at all levels +- [PR #1336](https://github.com/nf-core/rnaseq/pull/1336) - Use nf-core/setup-nf-test to install nf-test from cache during CI/CD - [PR #1340](https://github.com/nf-core/rnaseq/pull/1340) - Remove out-of-date Azure specific guidance - [PR #1341](https://github.com/nf-core/rnaseq/pull/1341) - Add rename in the MultiQC report for samples without techreps - [PR #1342](https://github.com/nf-core/rnaseq/pull/1342) - Factor out preprocessing - [PR #1345](https://github.com/nf-core/rnaseq/pull/1345) - Fix preprocessing call - [PR #1350](https://github.com/nf-core/rnaseq/pull/1350) - Reduce resource usage for sort process in bedtools/genomecov +- [PR #1352](https://github.com/nf-core/rnaseq/pull/1352) - Assorted fixes to MultiQC usage - [PR #1353](https://github.com/nf-core/rnaseq/pull/1353) - Correct conditional for salmon indexing in preprocessing workflow +- [PR #1355](https://github.com/nf-core/rnaseq/pull/1355) - Make all curves on subway map better looking, and all lines now have the same width +- [PR #1357](https://github.com/nf-core/rnaseq/pull/1357) - Fix anchor issue in multiqc +- [PR #1358](https://github.com/nf-core/rnaseq/pull/1358) - Update test profiles to restore a static URI for megatests +- [PR #1359](https://github.com/nf-core/rnaseq/pull/1359) - Update MultiQC and revert unnecessary workaround +- [PR #1360](https://github.com/nf-core/rnaseq/pull/1360) - More complete snapshots for pipeline level tests +- [PR #1361](https://github.com/nf-core/rnaseq/pull/1361) - Animate subway map +- [PR #1362](https://github.com/nf-core/rnaseq/pull/1362) - Move multiqc module prefix for nf-test to module +- [PR #1363](https://github.com/nf-core/rnaseq/pull/1363) - Minor updates of nf-core modules and subworkflows +- [PR #1363](https://github.com/nf-core/rnaseq/pull/1363) - Update dupradar script +- [PR #1366](https://github.com/nf-core/rnaseq/pull/1366) - Clarify docs on different tximport count files +- [PR #1367](https://github.com/nf-core/rnaseq/pull/1367) - Clarify design formula and blind dispersion estimation +- [PR #1370](https://github.com/nf-core/rnaseq/pull/1370) - Bump versions for 3.15.0 +- [PR #1371](https://github.com/nf-core/rnaseq/pull/1371) - Apply Maxime's CHANGELOG edits +- [PR #1372](https://github.com/nf-core/rnaseq/pull/1372) - Bump tximeta/tximport for gene table row names fix ### Parameters @@ -135,6 +189,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements | `samtools` | 1.17 | 1.20 | | `sortmerna` | 4.3.4 | 4.3.6 | | `umi_tools` | 1.14 | 1.15 | +| `untar` | 1.3 | 1.34 | > **NB:** Dependency has been **updated** if both old and new version information is present. > From 68b9a2161883ebc462e0ca5b9370d50a1a0dc652 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Tue, 10 Sep 2024 10:20:55 -0400 Subject: [PATCH 032/100] Another changelog fix --- CHANGELOG.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0dbb374c5..2b85818b0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -38,8 +38,6 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements > > **NB:** Dependency has been **removed** if new version information isn't present. -### Credits - ## [[3.15.0](https://github.com/nf-core/rnaseq/releases/tag/3.15.0)] - 2024-09-04 ### Credits From 5d20e28c94d7579cf5b3808ff6436ae6b6d5abb3 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 10 Sep 2024 15:39:10 +0100 Subject: [PATCH 033/100] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e1976f761..89cc402bf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v3.16.0dev - [date] - [PR #1374](https://github.com/nf-core/rnaseq/pull/1374) - Bump pipeline version to 3.16.0dev +- [PR #1376](https://github.com/nf-core/rnaseq/pull/1376) - Fix invalid named parameter syntax ### Credits From b4332d919cf67f6dfcad140178cba205ec4b9954 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Tue, 10 Sep 2024 19:42:35 -0400 Subject: [PATCH 034/100] Linting fix --- CHANGELOG.md | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2b85818b0..0ce92667b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,12 +14,14 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1351](https://github.com/nf-core/rnaseq/pull/1351) - Adding Kraken2/Bracken on unaligned reads as an additional quality control step to detect sample contamination ### Parameters -| Old parameter | New parameter | -| ------------------ | `--contaminant_screening` | -| | `--kraken_db` | -| | `--save_kraken_assignments` | -| | `--save_kraken_unassigned` | -| | `--bracken_precision` | + +| Old parameter | New parameter | +| ------------- | --------------------------- | +| | `--contaminant_screening` | +| | `--kraken_db` | +| | `--save_kraken_assignments` | +| | `--save_kraken_unassigned` | +| | `--bracken_precision` | > **NB:** Parameter has been **updated** if both old and new parameter information is present. > **NB:** Parameter has been **added** if just the new parameter information is present. @@ -27,10 +29,10 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements ### Software dependencies -| Dependency | Old version | New version | -| -------------- | ----------- | ----------- | -| `Kraken2` | ----------- | 2.1.3 | -| `Bracken` | ----------- | 2.9 | +| Dependency | Old version | New version | +| ---------- | ----------- | ----------- | +| `Kraken2` | ----------- | 2.1.3 | +| `Bracken` | ----------- | 2.9 | > **NB:** Dependency has been **updated** if both old and new version information is present. > From eada63ddbe0f3b03a0ecacd2f890c2584fbdd51e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Sep 2024 09:57:36 +0200 Subject: [PATCH 035/100] make snapshot versions pretty --- tests/default.nf.test.snap | 183 ++++++++++++++++++++++++++++++++++++- tests/lib/UTILS.groovy | 2 +- 2 files changed, 181 insertions(+), 4 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 79b3ca290..01450bb72 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -266,7 +266,50 @@ }, "Params: default - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", + { + "BBMAP_BBSPLIT": { + "bbmap": 39.01 + }, + "CAT_FASTQ": { + "cat": 8.3 + }, + "CUSTOM_CATADDITIONALFASTA": { + "python": null + }, + "CUSTOM_GETCHROMSIZES": { + "getchromsizes": 1.2 + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GTF2BED": { + "perl": "5.26.2" + }, + "GTF_FILTER": { + "python": "3.9.5" + }, + "GUNZIP_ADDITIONAL_FASTA": { + "gunzip": 1.1 + }, + "GUNZIP_GTF": { + "gunzip": 1.1 + }, + "STAR_GENOMEGENERATE": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "TRIMGALORE": { + "trimgalore": "0.6.7", + "cutadapt": 3.4 + }, + "UNTAR_SALMON_INDEX": { + "untar": 1.34 + }, + "Workflow": { + "nf-core/rnaseq": "v3.16.0dev" + } + }, "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -932,7 +975,141 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" + { + "BBMAP_BBSPLIT": { + "bbmap": 39.01 + }, + "BEDTOOLS_GENOMECOV_FW": { + "bedtools": "2.31.1" + }, + "CAT_FASTQ": { + "cat": 8.3 + }, + "CUSTOM_CATADDITIONALFASTA": { + "python": "3.9.5" + }, + "CUSTOM_GETCHROMSIZES": { + "getchromsizes": 1.2 + }, + "CUSTOM_TX2GENE": { + "python": "3.9.5" + }, + "DESEQ2_QC_PSEUDO": { + "r-base": "4.0.3", + "bioconductor-deseq2": "1.28.0" + }, + "DESEQ2_QC_STAR_SALMON": { + "r-base": "4.0.3", + "bioconductor-deseq2": "1.28.0" + }, + "DUPRADAR": { + "bioconductor-dupradar": "1.32.0" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "FQ_SUBSAMPLE": { + "fq": "0.9.1 (2022-02-22)" + }, + "GTF2BED": { + "perl": "5.26.2" + }, + "GTF_FILTER": { + "python": "3.9.5" + }, + "GUNZIP_ADDITIONAL_FASTA": { + "gunzip": 1.1 + }, + "GUNZIP_GTF": { + "gunzip": 1.1 + }, + "MULTIQC_CUSTOM_BIOTYPE": { + "python": "3.9.5" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.1.1" + }, + "QUALIMAP_RNASEQ": { + "qualimap": 2.3 + }, + "RSEQC_BAMSTAT": { + "rseqc": "5.0.2" + }, + "RSEQC_INFEREXPERIMENT": { + "rseqc": "5.0.2" + }, + "RSEQC_INNERDISTANCE": { + "rseqc": "5.0.2" + }, + "RSEQC_JUNCTIONANNOTATION": { + "rseqc": "5.0.2" + }, + "RSEQC_JUNCTIONSATURATION": { + "rseqc": "5.0.2" + }, + "RSEQC_READDISTRIBUTION": { + "rseqc": "5.0.2" + }, + "RSEQC_READDUPLICATION": { + "rseqc": "5.0.2" + }, + "SALMON_QUANT": { + "salmon": "1.10.1" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": 1.2 + }, + "SAMTOOLS_IDXSTATS": { + "samtools": 1.2 + }, + "SAMTOOLS_INDEX": { + "samtools": 1.2 + }, + "SAMTOOLS_SORT": { + "samtools": 1.2 + }, + "SAMTOOLS_STATS": { + "samtools": 1.2 + }, + "SE_GENE": { + "bioconductor-summarizedexperiment": "1.32.0" + }, + "STAR_ALIGN": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "STAR_GENOMEGENERATE": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "STRINGTIE_STRINGTIE": { + "stringtie": "2.2.1" + }, + "SUBREAD_FEATURECOUNTS": { + "subread": "2.0.1" + }, + "TRIMGALORE": { + "trimgalore": "0.6.7", + "cutadapt": 3.4 + }, + "TXIMETA_TXIMPORT": { + "bioconductor-tximeta": "1.20.1" + }, + "UCSC_BEDCLIP": { + "ucsc": 377 + }, + "UCSC_BEDGRAPHTOBIGWIG": { + "ucsc": 445 + }, + "UNTAR_SALMON_INDEX": { + "untar": 1.34 + }, + "Workflow": { + "nf-core/rnaseq": "v3.16.0dev" + } + } ], "meta": { "nf-test": "0.9.0", @@ -1077,4 +1254,4 @@ }, "timestamp": "2024-08-26T12:44:57.740534" } -} \ No newline at end of file +} diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index 1bd58a496..b5110dbf2 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -1,7 +1,7 @@ // Function to remove Nextflow version from pipeline_software_mqc_versions.yml class UTILS { - public static String removeNextflowVersion(pipeline_software_mqc_versions) { + public static Object removeNextflowVersion(pipeline_software_mqc_versions) { def softwareVersions = path(pipeline_software_mqc_versions).yaml if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") From e56788957559841b5688f86be11371789a48abed Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Sep 2024 10:06:08 +0200 Subject: [PATCH 036/100] update CHANGELOG --- CHANGELOG.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e1976f761..16df739e7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,14 +5,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v3.16.0dev - [date] -- [PR #1374](https://github.com/nf-core/rnaseq/pull/1374) - Bump pipeline version to 3.16.0dev - ### Credits Special thanks to the following for their contributions to the release: ### Enhancements & fixes +- [PR #1374](https://github.com/nf-core/rnaseq/pull/1374) - Bump pipeline version to 3.16.0dev +- [PR #1379](https://github.com/nf-core/rnaseq/pull/1379) - Make pipeline level test versions snapshots pretty + ## [[3.15.0](https://github.com/nf-core/rnaseq/releases/tag/3.15.0)] - 2024-09-04 ### Credits From c652e7945b0689d0b603067ff31dc93db3850c0e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Sep 2024 12:53:44 +0200 Subject: [PATCH 037/100] update all snapshots --- tests/default.nf.test | 936 +------ tests/default.nf.test.snap | 2442 +++++++++-------- tests/featurecounts_group_type.nf.test | 906 +------ tests/featurecounts_group_type.nf.test.snap | 2533 +++++++++++------- tests/hisat2.nf.test | 834 +----- tests/hisat2.nf.test.snap | 2330 +++++++++------- tests/kallisto.nf.test | 194 +- tests/kallisto.nf.test.snap | 577 ++-- tests/lib/UTILS.groovy | 49 +- tests/min_mapped_reads.nf.test | 825 +----- tests/min_mapped_reads.nf.test.snap | 2310 +++++++++------- tests/remove_ribo_rna.nf.test | 951 +------ tests/remove_ribo_rna.nf.test.snap | 2666 +++++++++++-------- tests/salmon.nf.test | 244 +- tests/salmon.nf.test.snap | 691 +++-- tests/skip_qc.nf.test | 500 +--- tests/skip_qc.nf.test.snap | 1374 ++++++---- tests/skip_trimming.nf.test | 816 +----- tests/skip_trimming.nf.test.snap | 2282 +++++++++------- tests/star_rsem.nf.test | 892 +------ tests/star_rsem.nf.test.snap | 2472 ++++++++++------- 21 files changed, 11754 insertions(+), 15070 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 069bb846f..e641012c5 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -12,908 +12,16 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name - ).match("bbsplit") }, - { assert snapshot( - path("${params.outdir}/custom/out/genome_gfp.fasta"), - path("${params.outdir}/custom/out/genome_gfp.gtf") - ).match("references") }, - { assert snapshot( - // HTMLs and ZIPs are not stable - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name - ).match("fastqc/raw") }, - { assert snapshot( - // HTMLs and ZIPs are not stable - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name - ).match("fastqc/trim") }, - { assert snapshot( - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), - // These files are not stable - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name - ).match("multiqc_data") }, - { assert snapshot( - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), - // PDFs, SVGs, some PNGs and HTML reports are not stable - file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_bam_stat.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name - ).match("multiqc_plots") }, - { assert snapshot( - path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"), - // These files are not stable - file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name - ).match("salmon/deseq2_qc") }, - { assert snapshot( - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), - // These files are not stable - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP1/quant.sf").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP2/quant.sf").name - ).match("salmon_quant") }, - { assert snapshot( - path("${params.outdir}/salmon/tx2gene.tsv"), - // These files are not stable - file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name - ).match("salmon") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig").name - ).match("star_salmon/bigwig") }, - { assert snapshot( - path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), - // These files are not stable - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt").name - ).match("star_salmon/deseq2_qc") }, - { assert snapshot( - path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP1_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP2_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"), - // PDFs are not stable - file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP1_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP2_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name - ).match("star_salmon/dupradar") }, - { assert snapshot( - path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt"), - // These files are unstable - file("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name, - file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name, - file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name, - file("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt.summary").name, - file("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt.summary").name - ).match("star_salmon/featurecounts") }, + { assert workflow.success}, { assert snapshot( - path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"), - // Logs are not stable - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name - ).match("star_salmon/log") }, - { assert snapshot( - // Metrics are not stable - file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name - ).match("star_salmon/picard_metrics") }, - { assert snapshot( - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - // HTML reports and these files are not stable - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt").name - ).match("star_salmon/qualimap") }, - { assert snapshot( - path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), - // PDFs, R scripts and all these files are not stable - file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name - ).match("star_salmon/rseqc") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name - ).match("star_salmon/salmon") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name - ).match("star_salmon/samtools_stats") }, - { assert snapshot( - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab"), - // These files are not stable - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf").name - ).match("star_salmon/stringtie") }, - { assert snapshot( - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name - ).match("star_salmon/markdup") }, - { assert snapshot( - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"), - path("${params.outdir}/star_salmon/tx2gene.tsv"), - // These files are not stable - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name, - file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name, - file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name - ).match("star_salmon/salmon_quant") }, - { assert snapshot( - // These reports are not stable - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name - ).match("trimgalore") }, - { assert snapshot( - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") - ).match("versions") } + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file_complement.collect { it.getName() }, + snapshottable_files + ).match() } ) } } @@ -929,31 +37,15 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, + { assert workflow.success}, { assert snapshot( UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, - file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + file_complement.collect { it.getName() }, + snapshottable_files ).match() } ) } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 01450bb72..2b4e1e8bc 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,269 +1,4 @@ { - "star_salmon/log": { - "content": [ - "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", - "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", - "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", - "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204", - "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23", - "RAP1_IAA_30M_REP1.Log.final.out", - "RAP1_IAA_30M_REP1.Log.out", - "RAP1_IAA_30M_REP1.Log.progress.out", - "RAP1_UNINDUCED_REP1.Log.final.out", - "RAP1_UNINDUCED_REP1.Log.out", - "RAP1_UNINDUCED_REP1.Log.progress.out", - "RAP1_UNINDUCED_REP2.Log.final.out", - "RAP1_UNINDUCED_REP2.Log.out", - "RAP1_UNINDUCED_REP2.Log.progress.out", - "WT_REP1.Log.final.out", - "WT_REP1.Log.out", - "WT_REP1.Log.progress.out", - "WT_REP2.Log.final.out", - "WT_REP2.Log.out", - "WT_REP2.Log.progress.out" - ], - "meta": { - 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"multiqc_salmon.txt:md5,c7368ba3d628d55d14a48a1664d0deca", + "multiqc_salmon_deseq2_clustering-plot.txt:md5,c39fd219828df33259e48aadcdd1997c", + "multiqc_salmon_deseq2_clustering-plot_1.txt:md5,6ccabfcdd11d36e140a7d6615c73ae85", + "multiqc_salmon_deseq2_clustering-plot_2.txt:md5,792ce8a58aefbbd10c0f182fcbc37c7a", + "multiqc_salmon_deseq2_clustering-plot_3.txt:md5,3080d13dee6e437084f27937296ede8a", + "multiqc_salmon_deseq2_clustering-plot_4.txt:md5,c750d2fa8d6dc8a2370335a71d2fa637", + "multiqc_salmon_deseq2_pca-plot.txt:md5,831426c001fe69be0e1ab2bfe32a234b", + "multiqc_samtools_flagstat.txt:md5,58b88d6bd59c226507d971fd9638405b", + "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", + "multiqc_samtools_stats.txt:md5,ad855d27b46822dbb701621fad3cc43f", + "multiqc_star.txt:md5,b3dc9dd2d290f12b8835758654a29edd", + "multiqc_star_salmon_deseq2_clustering-plot.txt:md5,72d5b6d429709160351d875524a50a7c", + "multiqc_star_salmon_deseq2_clustering-plot_1.txt:md5,37a19cbfb14a04455b57b6160d4ef25e", + "multiqc_star_salmon_deseq2_clustering-plot_2.txt:md5,ebad3b29617432485579000fb421958b", + "multiqc_star_salmon_deseq2_clustering-plot_3.txt:md5,0623170a882f18ef18387da6df69a650", + "multiqc_star_salmon_deseq2_clustering-plot_4.txt:md5,ebaa497884793b38eef593d98516ecc9", + "multiqc_star_salmon_deseq2_pca-plot.txt:md5,be897cdf8bba2b37249925f42a3dceae", + "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", + "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "qualimap_gene_coverage_profile_Counts.txt:md5,02044ed1bf1eca19a8a87c9971cdc049", + "qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa", + "qualimap_genomic_origin.txt:md5,bf9f1cba02195a298fb54c984c3269a6", + "qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce", + "qualimap_rnaseq_genome_results.txt:md5,ce5f4f7f5afa8f1e5666f738c4f414e7", + "rnaseq_qc_results.txt:md5,6bb8c2b18eb67b015bba7d92944cd687", + "rnaseq_qc_results.txt:md5,3eed764ef657161586b04670aad512d6", + "rnaseq_qc_results.txt:md5,401d4141bd4d884b35faa4cb497311f7", + "rnaseq_qc_results.txt:md5,fdf42ac95316d03a8ed66ab87d1b3d23", + "rnaseq_qc_results.txt:md5,9c6543bf977cea9624aab0d2c0eb2640", + "rseqc_bam_stat.txt:md5,ba2575875efaf137f8bf7c2b790d5b1b", + "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", + "rseqc_inner_distance.txt:md5,33a445ddf5841156362e908d62ab2a81", + "rseqc_inner_distance_plot_Counts.txt:md5,04561343fab91ad7e1e285f5816cf740", + "rseqc_inner_distance_plot_Percentages.txt:md5,92f40f2969a02e28a70b94ae78be045a", + "rseqc_junction_annotation_junctions_plot_Events.txt:md5,90f1fabea84aa36f647b980978d01e58", + "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,454eb9917793890ee4837fce43e3a8dd", + "rseqc_junction_saturation_all.txt:md5,144763c0da8891088ac98cf9b316cb5b", + "rseqc_junction_saturation_plot_All_Junctions.txt:md5,91ab7eac92f93e516ffc01a87977eba4", + "rseqc_junction_saturation_plot_Known_Junctions.txt:md5,0a405852c4b74c2031b782792baf4185", + "rseqc_junction_saturation_plot_Novel_Junctions.txt:md5,1daf2f820278df5a983be82bb0908271", + "rseqc_read_distribution_plot.txt:md5,48cea394a38d0f0ed3044b0a54638e65", + "rseqc_read_dups.txt:md5,e2df2dfd0a1acf5466c4b430330e15cd", + "rseqc_read_dups_plot.txt:md5,a9f437a3a7eaeb2709fa63644de16ea0", + "salmon.merged.gene_counts.tsv:md5,c14cab7e15cfac73ec0602dc2c404551", + "salmon.merged.gene_counts.tsv:md5,409576c08b219c6042cd9ee6865e6eac", + "salmon.merged.gene_counts_length_scaled.tsv:md5,a5ab2399bad77aea792b573d9aa2d2a9", + "salmon.merged.gene_counts_length_scaled.tsv:md5,880121f4cd7018d570df5a358c537df7", + "salmon.merged.gene_counts_scaled.tsv:md5,03c19bcf24070b5d2fc34d9dba1cd5f1", + "salmon.merged.gene_counts_scaled.tsv:md5,16d3e8dbeeb9710ebc208f8500b8687e", + "salmon.merged.gene_lengths.tsv:md5,de21d96e853159c7a2aff17cb1561800", + "salmon.merged.gene_lengths.tsv:md5,51e6035807aaaf5cdef3be3b906a65d9", + "salmon.merged.gene_tpm.tsv:md5,750651ebf5c4eb9e6ee9d49884ae6ab1", + "salmon.merged.gene_tpm.tsv:md5,5de927eec799249ef500f854a8096a2a", + "salmon.merged.transcript_counts.tsv:md5,ff0f5be09ca7a322672c0074ba35da17", + "salmon.merged.transcript_counts.tsv:md5,f5a3b4ee4edf754809792170f6a298e3", + "salmon.merged.transcript_lengths.tsv:md5,365c48741fe7b4978cd9a41c06523a21", + "salmon.merged.transcript_lengths.tsv:md5,0573be60d15c96f8aff8e01de650d5a3", + "salmon.merged.transcript_tpm.tsv:md5,6cf7047adabdd6084f4e273f54627214", + "salmon.merged.transcript_tpm.tsv:md5,ac804d1e2c4c344637449b1b62119a14", + "salmon_plot.txt:md5,5ec8f191683341725ad78425052bdc24", + "samtools-flagstat-dp_Percentage_of_total.txt:md5,4539f2d516dd8041a89468b71f1bc44f", + "samtools-flagstat-dp_Read_counts.txt:md5,382a459fe7651ed28fdf2923873a4564", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "samtools-stats-dp.txt:md5,3ad92aaf2ee90b0813e44a63ed695551", + "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", + "star_alignment_plot.txt:md5,77fc30308bc1b75bcf6e99630fc15344", + "star_summary_table.txt:md5,188cd28a8f309eb7c095694d79920eda", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T12:44:57.740534" + "timestamp": "2024-09-13T11:08:19.790408" } -} +} \ No newline at end of file diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index 16794293b..d8da742fc 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -13,878 +13,16 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name - ).match("bbsplit") }, - { assert snapshot( - path("${params.outdir}/custom/out/genome_gfp.fasta"), - path("${params.outdir}/custom/out/genome_gfp.gtf") - ).match("references") }, - { assert snapshot( - // HTMLs and ZIPs are not stable - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name - ).match("fastqc/raw") }, - { assert snapshot( - // HTMLs and ZIPs are not stable - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name - ).match("fastqc/trim") }, - { assert snapshot( - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), - // These files are not stable - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name - ).match("multiqc_data") }, - { assert snapshot( - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), - // PDFs, SVGs, some PNGs and HTML reports are not stable - file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_bam_stat.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name - ).match("multiqc_plots") }, - { assert snapshot( - path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"), - // These files are not stable - file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name - ).match("salmon/deseq2_qc") }, - { assert snapshot( - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), - // These files are not stable - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP1/quant.sf").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP2/quant.sf").name - ).match("salmon_quant") }, - { assert snapshot( - path("${params.outdir}/salmon/tx2gene.tsv"), - // These files are not stable - file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name - ).match("salmon") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig").name - ).match("star_salmon/bigwig") }, - { assert snapshot( - path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), - // These files are not stable - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt").name - ).match("star_salmon/deseq2_qc") }, - { assert snapshot( - path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP1_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP2_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"), - // PDFs are not stable - file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP1_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP2_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name - ).match("star_salmon/dupradar") }, + { assert workflow.success}, { assert snapshot( - path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"), - // Logs are not stable - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name - ).match("star_salmon/log") }, - { assert snapshot( - // Metrics are not stable - file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name - ).match("star_salmon/picard_metrics") }, - { assert snapshot( - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - // HTML reports and these files are not stable - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt").name - ).match("star_salmon/qualimap") }, - { assert snapshot( - path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), - // PDFs, R scripts and all these files are not stable - file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name - ).match("star_salmon/rseqc") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name - ).match("star_salmon/salmon") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name - ).match("star_salmon/samtools_stats") }, - { assert snapshot( - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab"), - // These files are not stable - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf").name - ).match("star_salmon/stringtie") }, - { assert snapshot( - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name - ).match("star_salmon/markdup") }, - { assert snapshot( - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"), - path("${params.outdir}/star_salmon/tx2gene.tsv"), - // These files are not stable - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name, - file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name, - file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name - ).match("star_salmon/salmon_quant") }, - { assert snapshot( - // These reports are not stable - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name - ).match("trimgalore") }, - { assert snapshot( - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") - ).match("versions") } + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file_complement.collect { it.getName() }, + snapshottable_files + ).match() } ) } } @@ -901,31 +39,15 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, + { assert workflow.success}, { assert snapshot( UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, - file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + file_complement.collect { it.getName() }, + snapshottable_files ).match() } ) } diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 3a08ab907..925bd0df5 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -1,1044 +1,1523 @@ { - "star_salmon/log": { - "content": [ - "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", - "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", - "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", - "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204", - "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23", - "RAP1_IAA_30M_REP1.Log.final.out", - "RAP1_IAA_30M_REP1.Log.out", - "RAP1_IAA_30M_REP1.Log.progress.out", - "RAP1_UNINDUCED_REP1.Log.final.out", - "RAP1_UNINDUCED_REP1.Log.out", - "RAP1_UNINDUCED_REP1.Log.progress.out", - "RAP1_UNINDUCED_REP2.Log.final.out", - "RAP1_UNINDUCED_REP2.Log.out", - "RAP1_UNINDUCED_REP2.Log.progress.out", - "WT_REP1.Log.final.out", - "WT_REP1.Log.out", - "WT_REP1.Log.progress.out", - "WT_REP2.Log.final.out", - "WT_REP2.Log.out", - "WT_REP2.Log.progress.out" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-22T17:43:26.652121" - }, - "star_salmon/salmon_quant": { - "content": [ - "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", - "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", - "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", - "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", - "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", - "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T13:34:18.439694" - }, - "multiqc_data": { - "content": [ - "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", - "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", - "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", - "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", - "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", - "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", - "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e", - "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", - "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", - "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", - "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", - "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c", - "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", - "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", - "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", - "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "qualimap_gene_coverage_profile_Counts.txt:md5,02044ed1bf1eca19a8a87c9971cdc049", - "qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa", - "qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce", - "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", - "fastqc_top_overrepresented_sequences_table-1.txt", - "fastqc_top_overrepresented_sequences_table.txt", - "junction_saturation_known.txt", - "junction_saturation_novel.txt", - "multiqc_data.json", - "multiqc_dupradar-section-plot.txt", - "multiqc_fail_strand_check_table.txt", - "multiqc_general_stats.txt", - "multiqc_picard_dups.txt", - "multiqc_rseqc_bam_stat.txt", - "multiqc_rseqc_infer_experiment.txt", - "multiqc_rseqc_junction_annotation.txt", - "multiqc_rseqc_read_distribution.txt", - "multiqc_salmon.txt", - "multiqc_salmon_deseq2_clustering-plot.txt", - "multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc_salmon_deseq2_clustering-plot_4.txt", - "multiqc_salmon_deseq2_pca-plot.txt", - "multiqc_samtools_flagstat.txt", - "multiqc_samtools_stats.txt", - "multiqc_software_versions.txt", - "multiqc_sources.txt", - "multiqc_star.txt", - "multiqc_star_salmon_deseq2_clustering-plot.txt", - "multiqc_star_salmon_deseq2_clustering-plot_1.txt", - "multiqc_star_salmon_deseq2_clustering-plot_2.txt", - "multiqc_star_salmon_deseq2_clustering-plot_3.txt", - "multiqc_star_salmon_deseq2_clustering-plot_4.txt", - "multiqc_star_salmon_deseq2_pca-plot.txt", - "picard_deduplication.txt", - "qualimap_genomic_origin.txt", - "qualimap_rnaseq_genome_results.txt", - "rseqc_bam_stat.txt", - "rseqc_inner_distance.txt", - "rseqc_inner_distance_plot_Counts.txt", - "rseqc_inner_distance_plot_Percentages.txt", - "rseqc_junction_annotation_junctions_plot_Events.txt", - "rseqc_junction_annotation_junctions_plot_Junctions.txt", - "rseqc_junction_saturation_all.txt", - "rseqc_junction_saturation_plot_All_Junctions.txt", - "rseqc_junction_saturation_plot_Known_Junctions.txt", - "rseqc_junction_saturation_plot_Novel_Junctions.txt", - "rseqc_read_distribution_plot.txt", - "rseqc_read_dups.txt", - "rseqc_read_dups_plot.txt", - "salmon_plot.txt", - "samtools-flagstat-dp_Percentage_of_total.txt", - "samtools-flagstat-dp_Read_counts.txt", - "samtools-stats-dp.txt", - "samtools_alignment_plot.txt", - "star_alignment_plot.txt", - "star_summary_table.txt" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-26T18:50:10.937365" - }, - "trimgalore": { - "content": [ - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-22T17:43:26.995324" - }, - "star_salmon/rseqc": { - "content": [ - "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,169d25b95c008bebe9ce886fea6a4e33", - "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,2ca0ce0fd3204bd2cc4812c4655b1f1f", - "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,7d5705880188f9beab1939e08d6b8f40", - "WT_REP1.infer_experiment.txt:md5,bf0c137f5fca06e7c40e1984a1acb06d", - "WT_REP2.infer_experiment.txt:md5,82e23b329ee60709f343bc2d17d43b14", - "RAP1_IAA_30M_REP1.bam_stat.txt", - "RAP1_UNINDUCED_REP1.bam_stat.txt", - "RAP1_UNINDUCED_REP2.bam_stat.txt", - "WT_REP1.bam_stat.txt", - "WT_REP2.bam_stat.txt", - "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", - "WT_REP1.inner_distance_plot.pdf", - "WT_REP2.inner_distance_plot.pdf", - "RAP1_IAA_30M_REP1.inner_distance_plot.r", - "WT_REP1.inner_distance_plot.r", - "WT_REP2.inner_distance_plot.r", - "RAP1_IAA_30M_REP1.inner_distance.txt", - "RAP1_IAA_30M_REP1.inner_distance_freq.txt", - "RAP1_IAA_30M_REP1.inner_distance_mean.txt", - "WT_REP1.inner_distance.txt", - "WT_REP1.inner_distance_freq.txt", - "WT_REP1.inner_distance_mean.txt", - "WT_REP2.inner_distance.txt", - "WT_REP2.inner_distance_freq.txt", - "WT_REP2.inner_distance_mean.txt", - "RAP1_IAA_30M_REP1.junction.Interact.bed", - "RAP1_IAA_30M_REP1.junction.bed", - "RAP1_UNINDUCED_REP1.junction.Interact.bed", - "RAP1_UNINDUCED_REP1.junction.bed", - "RAP1_UNINDUCED_REP2.junction.Interact.bed", - "RAP1_UNINDUCED_REP2.junction.bed", - "WT_REP1.junction.Interact.bed", - "WT_REP1.junction.bed", - "WT_REP2.junction.Interact.bed", - "WT_REP2.junction.bed", - "RAP1_IAA_30M_REP1.junction_annotation.log", - "RAP1_UNINDUCED_REP1.junction_annotation.log", - "RAP1_UNINDUCED_REP2.junction_annotation.log", - "WT_REP1.junction_annotation.log", - "WT_REP2.junction_annotation.log", - "RAP1_IAA_30M_REP1.splice_events.pdf", - "RAP1_IAA_30M_REP1.splice_junction.pdf", - "RAP1_UNINDUCED_REP1.splice_events.pdf", - "RAP1_UNINDUCED_REP1.splice_junction.pdf", - "RAP1_UNINDUCED_REP2.splice_events.pdf", - "RAP1_UNINDUCED_REP2.splice_junction.pdf", - "WT_REP1.splice_events.pdf", - "WT_REP1.splice_junction.pdf", - "WT_REP2.splice_events.pdf", - "WT_REP2.splice_junction.pdf", - "RAP1_IAA_30M_REP1.junction_plot.r", - "RAP1_UNINDUCED_REP1.junction_plot.r", - "RAP1_UNINDUCED_REP2.junction_plot.r", - "WT_REP1.junction_plot.r", - "WT_REP2.junction_plot.r", - 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"coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211", + "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d", + "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b", + "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", + "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff", + "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", + "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", + "deseq2.pca.vals.txt:md5,1c67cac64dbcad0e8d83d84b5636c3e2", + "deseq2.pca.vals.txt:md5,159d70e157d4273cbf7121a06208a536", + "deseq2.sample.dists.txt:md5,5e9881e1e97a13230435e116dee981f9", + "deseq2.sample.dists.txt:md5,c27be3cc1cb2f5c6f663dfe7d538eff3", + "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", + "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", + "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", + "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", + "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", + "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", + "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", + "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c", + "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", + "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", + "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", + "fastqc_top_overrepresented_sequences_table-1.txt:md5,fbd6b1f651b8fbe108b05a19e9ba7ca7", + "fastqc_top_overrepresented_sequences_table.txt:md5,a415f85e91e40b3e33495c8966b589e6", + "flenDist.txt:md5,43ef9812ccd1c61c41fd03fe20b29e3e", + "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", + "flenDist.txt:md5,7de4516be3cc8d9339c9e245286ebaec", + "flenDist.txt:md5,944b7e9b011aa659848596d33a22991b", + "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", + "flenDist.txt:md5,83603c5784a7cddc304a7d0a53660c94", + "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", + "flenDist.txt:md5,b7808dd650470f30730f55819fe070fd", + "flenDist.txt:md5,0a0798ae1b15e73ccb2fe671dd0db1f5", + "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", + "junction_saturation_known.txt:md5,fc168116148ddc010e3247499e35b3a7", + "junction_saturation_novel.txt:md5,57499d7895d2af954961b7af98e26266", + "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", + "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", + "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", + "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", + "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", + "meta_info.json:md5,b539b9fa0b7a5698ecda991d8f92a860", + "meta_info.json:md5,d8608fb6439e5e0632acfc9d5681c755", + "meta_info.json:md5,13d7f9f021532a3f5b4ca3b1e04b1deb", + "meta_info.json:md5,49566d41ad3ed6db89e523a701bcef6e", + "meta_info.json:md5,92e033fdb0f51977392f1192b6b4f77b", + "meta_info.json:md5,cd51b8bedbafdc0123db4db59d2aaf7d", + "meta_info.json:md5,4bdc7b4d03bc6b4704eb04d89f9c36af", + "meta_info.json:md5,c1aabb3eb6a845eb578f222e6af48ae5", + "meta_info.json:md5,f606b889a0f98b4cf79cf2b5f1f9a9a5", + "meta_info.json:md5,707c0167c7800abf1a12b8f4437e4bfb", + "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", + "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_dupradar-section-plot.txt:md5,1bb6be44bf23ba406d1a44412eb255f5", + "multiqc_fail_strand_check_table.txt:md5,b73dd03ea0a10e270b1c7ff8871c38ba", + "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", + "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", + "multiqc_general_stats.txt:md5,9697b7b40b6852b095a990ce432d82e1", + "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", + "multiqc_rseqc_bam_stat.txt:md5,1aa9eeb5b9d283ba77e98f0f5ea0f712", + "multiqc_rseqc_infer_experiment.txt:md5,475b85d8065528e9674a74d2d43644ab", + "multiqc_rseqc_junction_annotation.txt:md5,e78e23f7f32cc2c58136df6ed89d7638", + "multiqc_rseqc_read_distribution.txt:md5,b7106d48346fe4150a8094ef1744f8b3", + "multiqc_salmon.txt:md5,daed924a3d9ba8d9bf35bad9d4ec07f9", + "multiqc_salmon_deseq2_clustering-plot.txt:md5,cf7bf557dfdcde533c599c435f566dce", + "multiqc_salmon_deseq2_clustering-plot_1.txt:md5,0685e6840b85aa4b36e1e3622bc91e4a", + "multiqc_salmon_deseq2_clustering-plot_2.txt:md5,90c0c2745c295fcc0a2fb9218281bec9", + "multiqc_salmon_deseq2_clustering-plot_3.txt:md5,ee5baadfcb9a9bbf375dc08fa6998b1c", + "multiqc_salmon_deseq2_clustering-plot_4.txt:md5,aa48c14dae0bcf9ee6b3f88142b156cb", + "multiqc_salmon_deseq2_pca-plot.txt:md5,301050113f8d404171c962f685d5b10b", + "multiqc_samtools_flagstat.txt:md5,c73d1a59c0c9e3a496e092cc4999ad6d", + "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", + "multiqc_samtools_stats.txt:md5,8f0c8097d48301461ac419cbf40b56b0", + "multiqc_star.txt:md5,ae82337a5f847c86e8ffe14e04dfeaee", + "multiqc_star_salmon_deseq2_clustering-plot.txt:md5,72d5b6d429709160351d875524a50a7c", + "multiqc_star_salmon_deseq2_clustering-plot_1.txt:md5,37a19cbfb14a04455b57b6160d4ef25e", + "multiqc_star_salmon_deseq2_clustering-plot_2.txt:md5,ebad3b29617432485579000fb421958b", + "multiqc_star_salmon_deseq2_clustering-plot_3.txt:md5,0623170a882f18ef18387da6df69a650", + "multiqc_star_salmon_deseq2_clustering-plot_4.txt:md5,ebaa497884793b38eef593d98516ecc9", + "multiqc_star_salmon_deseq2_pca-plot.txt:md5,be897cdf8bba2b37249925f42a3dceae", + "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", + "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "qualimap_gene_coverage_profile_Counts.txt:md5,02044ed1bf1eca19a8a87c9971cdc049", + "qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa", + "qualimap_genomic_origin.txt:md5,bf9f1cba02195a298fb54c984c3269a6", + "qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce", + "qualimap_rnaseq_genome_results.txt:md5,ce5f4f7f5afa8f1e5666f738c4f414e7", + "rnaseq_qc_results.txt:md5,6bb8c2b18eb67b015bba7d92944cd687", + "rnaseq_qc_results.txt:md5,3eed764ef657161586b04670aad512d6", + "rnaseq_qc_results.txt:md5,401d4141bd4d884b35faa4cb497311f7", + "rnaseq_qc_results.txt:md5,fdf42ac95316d03a8ed66ab87d1b3d23", + "rnaseq_qc_results.txt:md5,9c6543bf977cea9624aab0d2c0eb2640", + "rseqc_bam_stat.txt:md5,ba2575875efaf137f8bf7c2b790d5b1b", + "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", + "rseqc_inner_distance.txt:md5,19c55be80264821100f270661ac4937f", + "rseqc_inner_distance_plot_Counts.txt:md5,b8116ab4d78349e72a5d2ee3ca22597c", + "rseqc_inner_distance_plot_Percentages.txt:md5,2a9506bb04f2b661de081795cff17f46", + "rseqc_junction_annotation_junctions_plot_Events.txt:md5,90f1fabea84aa36f647b980978d01e58", + "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,454eb9917793890ee4837fce43e3a8dd", + "rseqc_junction_saturation_all.txt:md5,59d36ebefa6ea9568dadb8631a9325a7", + "rseqc_junction_saturation_plot_All_Junctions.txt:md5,28cdbb3a7bf6b52b39ad7e16f5df48ca", + "rseqc_junction_saturation_plot_Known_Junctions.txt:md5,e9be5dd2857abb8a15154b8435ecb915", + "rseqc_junction_saturation_plot_Novel_Junctions.txt:md5,35ebc2ccd7b77a51c7fff5ab9ea9d96c", + "rseqc_read_distribution_plot.txt:md5,48cea394a38d0f0ed3044b0a54638e65", + "rseqc_read_dups.txt:md5,28180affc24fcd67eda69be83d0825d2", + "rseqc_read_dups_plot.txt:md5,a9f437a3a7eaeb2709fa63644de16ea0", + "salmon.merged.gene_counts.tsv:md5,c14cab7e15cfac73ec0602dc2c404551", + "salmon.merged.gene_counts.tsv:md5,52bf9bce9175a6158b38f6dda338ad95", + "salmon.merged.gene_counts_length_scaled.tsv:md5,45ebc7b36ba8078aecd0fa187ea7f289", + "salmon.merged.gene_counts_length_scaled.tsv:md5,c3c6d4844e2d3e3edb77fd59d992d463", + "salmon.merged.gene_counts_scaled.tsv:md5,a6081c816f2476be1a8f25c6b569a441", + "salmon.merged.gene_counts_scaled.tsv:md5,31f3879878aa8157a04de604d650d0a2", + "salmon.merged.gene_lengths.tsv:md5,f45995c98ed1c30da09d1387c10b9480", + "salmon.merged.gene_lengths.tsv:md5,fbf847cbf9a23eb9b203c64ee209d5f1", + "salmon.merged.gene_tpm.tsv:md5,53a07196cb7b323f086a1f0e494ab929", + "salmon.merged.gene_tpm.tsv:md5,634b52e5978685de75abbf0cfb8b3b1e", + "salmon.merged.transcript_counts.tsv:md5,ff0f5be09ca7a322672c0074ba35da17", + "salmon.merged.transcript_counts.tsv:md5,ec4c48f1b1072a0e8e943e709c00e189", + "salmon.merged.transcript_lengths.tsv:md5,34c408ef2a80fbcd386c998bedaeca71", + "salmon.merged.transcript_lengths.tsv:md5,104b660bec01e6e014e21c2de239164e", + "salmon.merged.transcript_tpm.tsv:md5,c5786607417d24a0edd9c35c84b9d5e7", + "salmon.merged.transcript_tpm.tsv:md5,32961510c67426541f3729cd565ba5ab", + "salmon_plot.txt:md5,83ee202f66071102f1f7b5ae5c02f872", + "samtools-flagstat-dp_Percentage_of_total.txt:md5,fb2847aa158ce48ffd9fdd256afca29a", + "samtools-flagstat-dp_Read_counts.txt:md5,8de72682470e02ffab7362ec5b603fab", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "samtools-stats-dp.txt:md5,5f43f4096834e64f009d614b9e3aa9f3", + "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", + "star_alignment_plot.txt:md5,a44811c928719507cee0f98da7492fd1", + "star_summary_table.txt:md5,32aab6812d43f3c850b739eda99990f1", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T14:18:38.410297" + "timestamp": "2024-09-13T11:17:15.946467" } } \ No newline at end of file diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 9577086ea..3bde9696b 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -13,806 +13,16 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name - ).match("bbsplit") }, - { assert snapshot( - path("${params.outdir}/custom/out/genome_gfp.fasta"), - path("${params.outdir}/custom/out/genome_gfp.gtf") - ).match("references") }, - { assert snapshot( - // HTMLs and ZIPs are not stable - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name - ).match("fastqc/raw") }, - { assert snapshot( - // HTMLs and ZIPs are not stable - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name - ).match("fastqc/trim") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/hisat2/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name, - file("${params.outdir}/hisat2/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name, - file("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name, - file("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name, - file("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name, - file("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name, - file("${params.outdir}/hisat2/bigwig/WT_REP1.forward.bigWig").name, - file("${params.outdir}/hisat2/bigwig/WT_REP1.reverse.bigWig").name, - file("${params.outdir}/hisat2/bigwig/WT_REP2.forward.bigWig").name, - file("${params.outdir}/hisat2/bigwig/WT_REP2.reverse.bigWig").name - ).match("hisat2/bigwig") }, - { assert snapshot( - path("${params.outdir}/hisat2/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"), - path("${params.outdir}/hisat2/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"), - path("${params.outdir}/hisat2/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"), - path("${params.outdir}/hisat2/dupradar/gene_data/WT_REP1_dupMatrix.txt"), - path("${params.outdir}/hisat2/dupradar/gene_data/WT_REP2_dupMatrix.txt"), - path("${params.outdir}/hisat2/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"), - path("${params.outdir}/hisat2/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"), - path("${params.outdir}/hisat2/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"), - path("${params.outdir}/hisat2/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"), - path("${params.outdir}/hisat2/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"), - // PDFs are not stable - file("${params.outdir}/hisat2/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/hisat2/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/hisat2/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name, - file("${params.outdir}/hisat2/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/hisat2/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name, - file("${params.outdir}/hisat2/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name, - file("${params.outdir}/hisat2/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name, - file("${params.outdir}/hisat2/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name, - file("${params.outdir}/hisat2/dupradar/histogram/WT_REP1_expressionHist.pdf").name, - file("${params.outdir}/hisat2/dupradar/histogram/WT_REP2_expressionHist.pdf").name, - file("${params.outdir}/hisat2/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/hisat2/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/hisat2/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name, - file("${params.outdir}/hisat2/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/hisat2/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name - ).match("hisat2/dupradar") }, - { assert snapshot( - path("${params.outdir}/hisat2/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"), - path("${params.outdir}/hisat2/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/hisat2/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"), - path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"), - path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"), - path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"), - path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"), - path("${params.outdir}/hisat2/featurecounts/WT_REP1.biotype_counts_mqc.tsv"), - path("${params.outdir}/hisat2/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/hisat2/featurecounts/WT_REP1.featureCounts.txt"), - path("${params.outdir}/hisat2/featurecounts/WT_REP2.biotype_counts_mqc.tsv"), - path("${params.outdir}/hisat2/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/hisat2/featurecounts/WT_REP2.featureCounts.txt"), - file("${params.outdir}/hisat2/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name, - file("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name, - file("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name, - file("${params.outdir}/hisat2/featurecounts/WT_REP1.featureCounts.txt.summary").name, - file("${params.outdir}/hisat2/featurecounts/WT_REP2.featureCounts.txt.summary").name - ).match("hisat2/featurecounts") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/hisat2/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, - file("${params.outdir}/hisat2/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/hisat2/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, - file("${params.outdir}/hisat2/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/hisat2/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, - file("${params.outdir}/hisat2/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, - file("${params.outdir}/hisat2/WT_REP1.markdup.sorted.bam").name, - file("${params.outdir}/hisat2/WT_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/hisat2/WT_REP2.markdup.sorted.bam").name, - file("${params.outdir}/hisat2/WT_REP2.markdup.sorted.bam.bai").name - ).match("hisat2/markdup") }, - { assert snapshot( - file("${params.outdir}/hisat2/log/RAP1_IAA_30M_REP1.hisat2.summary.log").name, - file("${params.outdir}/hisat2/log/RAP1_UNINDUCED_REP1.hisat2.summary.log").name, - file("${params.outdir}/hisat2/log/RAP1_UNINDUCED_REP2.hisat2.summary.log").name, - file("${params.outdir}/hisat2/log/WT_REP1.hisat2.summary.log").name, - file("${params.outdir}/hisat2/log/WT_REP2.hisat2.summary.log").name - ).match("hisat2") }, - { assert snapshot( - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc-status-check-heatmap-1.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc-status-check-heatmap.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_adapter_content_plot.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_sequence_counts_plot.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_citations.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_cutadapt.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_histogram.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_histogram_1.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_histogram_2.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), - // These files are not stable - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/hisat2_pe_plot.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/hisat2_se_plot.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/junction_saturation_known.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/junction_saturation_novel.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_data.json").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_general_stats.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_1.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_2.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_3.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_4.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_pca-plot.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_picard_dups.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_samtools_flagstat.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_samtools_stats.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_software_versions.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_sources.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_deduplication.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_genomic_origin.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_bam_stat.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_all.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_read_distribution_plot.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_read_dups.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_read_dups_plot.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/salmon_plot.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-stats-dp.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools_alignment_plot.txt").name - ).match("multiqc_data") }, - { assert snapshot( - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/dupradar-section-plot.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_read_dups_plot.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), - // PDFs, SVGs, some PNGs and HTML reports are not stable - file("${params.outdir}/multiqc/hisat2/multiqc_report.html").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/general_stats_table.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_deseq2_pca-plot.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_pe_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_pe_plot-pct.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_se_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_se_plot-pct.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/salmon_plot.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fail_strand_check_table.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/general_stats_table.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_deseq2_clustering-plot.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_deseq2_pca-plot.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_pe_plot-cnt.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_pe_plot-pct.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_se_plot-cnt.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_se_plot-pct.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/picard_deduplication-cnt.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/picard_deduplication-pct.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_bam_stat.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/salmon_plot.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-stats-dp.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/dupradar-section-plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fail_strand_check_table.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/general_stats_table.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_deseq2_clustering-plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_deseq2_pca-plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-cnt.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-pct.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_se_plot-cnt.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_se_plot-pct.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/picard_deduplication-pct.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_bam_stat.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/salmon_plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-stats-dp.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name - ).match("multiqc_plots") }, + { assert workflow.success}, { assert snapshot( - // Metrics are not stable - file("${params.outdir}/hisat2/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/hisat2/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/hisat2/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/hisat2/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/hisat2/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name - ).match("hisat2/picard_metrics") }, - { assert snapshot( - path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/hisat2/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/hisat2/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/hisat2/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/hisat2/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/hisat2/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/hisat2/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - // HTML reports and these files are not stable - file("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, - file("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, - file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, - file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name, - file("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/hisat2/qualimap/WT_REP1/qualimapReport.html").name, - file("${params.outdir}/hisat2/qualimap/WT_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/hisat2/qualimap/WT_REP2/qualimapReport.html").name, - file("${params.outdir}/hisat2/qualimap/WT_REP2/rnaseq_qc_results.txt").name - ).match("hisat2/qualimap") }, - { assert snapshot( - path("${params.outdir}/hisat2/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), - path("${params.outdir}/hisat2/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), - path("${params.outdir}/hisat2/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), - path("${params.outdir}/hisat2/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), - path("${params.outdir}/hisat2/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), - // PDFs, R scripts and all these files are not stable - file("${params.outdir}/hisat2/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name, - file("${params.outdir}/hisat2/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name, - file("${params.outdir}/hisat2/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name, - file("${params.outdir}/hisat2/rseqc/bam_stat/WT_REP1.bam_stat.txt").name, - file("${params.outdir}/hisat2/rseqc/bam_stat/WT_REP2.bam_stat.txt").name, - file("${params.outdir}/hisat2/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, - file("${params.outdir}/hisat2/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name, - file("${params.outdir}/hisat2/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name, - file("${params.outdir}/hisat2/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name, - file("${params.outdir}/hisat2/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name, - file("${params.outdir}/hisat2/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name, - file("${params.outdir}/hisat2/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name, - file("${params.outdir}/hisat2/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name, - file("${params.outdir}/hisat2/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name, - file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name, - file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name, - file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name, - file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name, - file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name, - file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name, - file("${params.outdir}/hisat2/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name, - file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, - file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name, - file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, - file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name, - file("${params.outdir}/hisat2/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name, - file("${params.outdir}/hisat2/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name, - file("${params.outdir}/hisat2/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name, - file("${params.outdir}/hisat2/rseqc/read_distribution/WT_REP1.read_distribution.txt").name, - file("${params.outdir}/hisat2/rseqc/read_distribution/WT_REP2.read_distribution.txt").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name - ).match("hisat2/rseqc") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, - file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, - file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, - file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name, - file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name, - file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, - file("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.stats").name, - file("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, - file("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.flagstat").name, - file("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.idxstats").name, - file("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.stats").name - ).match("hisat2/samtools_stats") }, - { assert snapshot( - path("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"), - path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"), - path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"), - path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"), - path("${params.outdir}/hisat2/stringtie/WT_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/hisat2/stringtie/WT_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/hisat2/stringtie/WT_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/hisat2/stringtie/WT_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/hisat2/stringtie/WT_REP2.ballgown/e2t.ctab"), - path("${params.outdir}/hisat2/stringtie/WT_REP2.ballgown/e_data.ctab"), - path("${params.outdir}/hisat2/stringtie/WT_REP2.ballgown/i2t.ctab"), - path("${params.outdir}/hisat2/stringtie/WT_REP2.ballgown/i_data.ctab"), - // These files are not stable - file("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name, - file("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name, - file("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name, - file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name, - file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name, - file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name, - file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name, - file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name, - file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name, - file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name, - file("${params.outdir}/hisat2/stringtie/WT_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/hisat2/stringtie/WT_REP1.coverage.gtf").name, - file("${params.outdir}/hisat2/stringtie/WT_REP1.gene.abundance.txt").name, - file("${params.outdir}/hisat2/stringtie/WT_REP1.transcripts.gtf").name, - file("${params.outdir}/hisat2/stringtie/WT_REP2.ballgown/t_data.ctab").name, - file("${params.outdir}/hisat2/stringtie/WT_REP2.coverage.gtf").name, - file("${params.outdir}/hisat2/stringtie/WT_REP2.gene.abundance.txt").name, - file("${params.outdir}/hisat2/stringtie/WT_REP2.transcripts.gtf").name - ).match("hisat2/stringtie") }, - { assert snapshot( - path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"), - // These files are not stable - file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name - ).match("salmon/deseq2_qc") }, - { assert snapshot( - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), - // These files are not stable - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP1/quant.sf").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP2/quant.sf").name - ).match("salmon_quant") }, - { assert snapshot( - path("${params.outdir}/salmon/tx2gene.tsv"), - // These files are not stable - file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name - ).match("salmon") }, - { assert snapshot( - // These reports are not stable - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name - ).match("trimgalore") }, - { assert snapshot( - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") - ).match("versions") } + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file_complement.collect { it.getName() }, + snapshottable_files + ).match() } ) } } @@ -829,31 +39,15 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, + { assert workflow.success}, { assert snapshot( UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, - file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report.html").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + file_complement.collect { it.getName() }, + snapshottable_files ).match() } ) } diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 1a15dd9a4..7bc3666ce 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -1,961 +1,1403 @@ { - "hisat2/rseqc": { - "content": [ - "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,1d4348685fa61819ff8076213d0873b3", - "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,3ee0f64e82f0b1ac16b5f3e2b30b024c", - "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,3d17628d178e5a3cc9dc03f32614bff7", - "WT_REP1.infer_experiment.txt:md5,13e3c748f5b968455a39eb9fefd87053", - "WT_REP2.infer_experiment.txt:md5,230910b354a5531d1c4bf711ccd6e493", - "RAP1_IAA_30M_REP1.bam_stat.txt", - "RAP1_UNINDUCED_REP1.bam_stat.txt", - "RAP1_UNINDUCED_REP2.bam_stat.txt", - "WT_REP1.bam_stat.txt", - "WT_REP2.bam_stat.txt", - "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", - "WT_REP1.inner_distance_plot.pdf", - "WT_REP2.inner_distance_plot.pdf", - "RAP1_IAA_30M_REP1.inner_distance_plot.r", - "WT_REP1.inner_distance_plot.r", - "WT_REP2.inner_distance_plot.r", - "RAP1_IAA_30M_REP1.inner_distance.txt", - "RAP1_IAA_30M_REP1.inner_distance_freq.txt", - "RAP1_IAA_30M_REP1.inner_distance_mean.txt", - "WT_REP1.inner_distance.txt", - "WT_REP1.inner_distance_freq.txt", - "WT_REP1.inner_distance_mean.txt", - "WT_REP2.inner_distance.txt", - "WT_REP2.inner_distance_freq.txt", - "WT_REP2.inner_distance_mean.txt", - "RAP1_IAA_30M_REP1.junction.Interact.bed", - "RAP1_IAA_30M_REP1.junction.bed", - "RAP1_UNINDUCED_REP1.junction.Interact.bed", - "RAP1_UNINDUCED_REP1.junction.bed", - "RAP1_UNINDUCED_REP2.junction.Interact.bed", - "RAP1_UNINDUCED_REP2.junction.bed", - "WT_REP1.junction.Interact.bed", - "WT_REP1.junction.bed", - "WT_REP2.junction.Interact.bed", - "WT_REP2.junction.bed", - "RAP1_IAA_30M_REP1.junction_annotation.log", - "RAP1_UNINDUCED_REP1.junction_annotation.log", - "RAP1_UNINDUCED_REP2.junction_annotation.log", - "WT_REP1.junction_annotation.log", - "WT_REP2.junction_annotation.log", - "RAP1_IAA_30M_REP1.splice_events.pdf", - "RAP1_IAA_30M_REP1.splice_junction.pdf", - "RAP1_UNINDUCED_REP1.splice_events.pdf", - "RAP1_UNINDUCED_REP1.splice_junction.pdf", - "RAP1_UNINDUCED_REP2.splice_events.pdf", - "RAP1_UNINDUCED_REP2.splice_junction.pdf", - "WT_REP1.splice_events.pdf", - "WT_REP1.splice_junction.pdf", - "WT_REP2.splice_events.pdf", - "WT_REP2.splice_junction.pdf", - "RAP1_IAA_30M_REP1.junction_plot.r", - "RAP1_UNINDUCED_REP1.junction_plot.r", - "RAP1_UNINDUCED_REP2.junction_plot.r", - "WT_REP1.junction_plot.r", - "WT_REP2.junction_plot.r", - "RAP1_IAA_30M_REP1.junction.xls", - "RAP1_UNINDUCED_REP1.junction.xls", - "RAP1_UNINDUCED_REP2.junction.xls", - "WT_REP1.junction.xls", - "WT_REP2.junction.xls", - "RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf", - "RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf", - "RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf", - "WT_REP1.junctionSaturation_plot.pdf", - "WT_REP2.junctionSaturation_plot.pdf", - "RAP1_IAA_30M_REP1.junctionSaturation_plot.r", - "RAP1_UNINDUCED_REP1.junctionSaturation_plot.r", - "RAP1_UNINDUCED_REP2.junctionSaturation_plot.r", - "WT_REP1.junctionSaturation_plot.r", - "WT_REP2.junctionSaturation_plot.r", - "RAP1_IAA_30M_REP1.read_distribution.txt", - "RAP1_UNINDUCED_REP1.read_distribution.txt", - "RAP1_UNINDUCED_REP2.read_distribution.txt", - "WT_REP1.read_distribution.txt", - "WT_REP2.read_distribution.txt", - "RAP1_IAA_30M_REP1.DupRate_plot.pdf", - "RAP1_UNINDUCED_REP1.DupRate_plot.pdf", - "RAP1_UNINDUCED_REP2.DupRate_plot.pdf", - "WT_REP1.DupRate_plot.pdf", - "WT_REP2.DupRate_plot.pdf", - "RAP1_IAA_30M_REP1.DupRate_plot.r", - "RAP1_UNINDUCED_REP1.DupRate_plot.r", - "RAP1_UNINDUCED_REP2.DupRate_plot.r", - "WT_REP1.DupRate_plot.r", - "WT_REP2.DupRate_plot.r", - "RAP1_IAA_30M_REP1.pos.DupRate.xls", - "RAP1_IAA_30M_REP1.seq.DupRate.xls", - "RAP1_UNINDUCED_REP1.pos.DupRate.xls", - "RAP1_UNINDUCED_REP1.seq.DupRate.xls", - "RAP1_UNINDUCED_REP2.pos.DupRate.xls", - "RAP1_UNINDUCED_REP2.seq.DupRate.xls", - "WT_REP1.pos.DupRate.xls", - "WT_REP1.seq.DupRate.xls", - "WT_REP2.pos.DupRate.xls", - "WT_REP2.seq.DupRate.xls" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-26T13:55:07.472724" - }, - "trimgalore": { - "content": [ - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T10:32:15.607595" - }, - "multiqc_data": { - "content": [ - "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", - "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", - "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", - "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", - "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", - "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", - "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e", - "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", - "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", - "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", - "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", - "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c", - "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", - "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", - "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", - "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "multiqc_citations.txt:md5,da5043f8ab9b5bd51d91ccf3111c655e", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "multiqc_featurecounts_biotype_plot.txt:md5,d35ad008181f0f7be84d5770d17a3a65", - "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "qualimap_gene_coverage_profile_Counts.txt:md5,f3b9bb1902af4c7b5e04c0830ded2c02", - "qualimap_gene_coverage_profile_Normalised.txt:md5,ebcedec8e5c959414a4e89ccae3fc07e", - "qualimap_rnaseq_cov_hist.txt:md5,b78ff616f267f9b061b3297b767e88fb", - "rseqc_infer_experiment_plot.txt:md5,0556a013129be7d78fac4345fddbe8c5", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3625f666cc09d0f07990716aeccd869f", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,6c323b383a6506d124506405b9463d93", - "fastqc_top_overrepresented_sequences_table-1.txt", - "fastqc_top_overrepresented_sequences_table.txt", - "hisat2_pe_plot.txt", - "hisat2_se_plot.txt", - "junction_saturation_known.txt", - "junction_saturation_novel.txt", - "multiqc_data.json", - "multiqc_dupradar-section-plot.txt", - "multiqc_fail_strand_check_table.txt", - "multiqc_general_stats.txt", - "multiqc_hisat2.txt", - "multiqc_hisat2_deseq2_clustering-plot.txt", - "multiqc_hisat2_deseq2_clustering-plot_1.txt", - "multiqc_hisat2_deseq2_clustering-plot_2.txt", - "multiqc_hisat2_deseq2_clustering-plot_3.txt", - "multiqc_hisat2_deseq2_clustering-plot_4.txt", - "multiqc_hisat2_deseq2_pca-plot.txt", - "multiqc_picard_dups.txt", - "multiqc_rseqc_bam_stat.txt", - "multiqc_rseqc_infer_experiment.txt", - "multiqc_rseqc_junction_annotation.txt", - "multiqc_rseqc_read_distribution.txt", - "multiqc_salmon.txt", - "multiqc_salmon_deseq2_clustering-plot.txt", - "multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc_salmon_deseq2_clustering-plot_4.txt", - "multiqc_salmon_deseq2_pca-plot.txt", - "multiqc_samtools_flagstat.txt", - "multiqc_samtools_stats.txt", - "multiqc_software_versions.txt", - "multiqc_sources.txt", - "picard_deduplication.txt", - "qualimap_genomic_origin.txt", - "rseqc_bam_stat.txt", - "rseqc_inner_distance.txt", - "rseqc_inner_distance_plot_Counts.txt", - "rseqc_inner_distance_plot_Percentages.txt", - "rseqc_junction_annotation_junctions_plot_Events.txt", - "rseqc_junction_annotation_junctions_plot_Junctions.txt", - "rseqc_junction_saturation_all.txt", - "rseqc_junction_saturation_plot_All_Junctions.txt", - "rseqc_junction_saturation_plot_Known_Junctions.txt", - "rseqc_junction_saturation_plot_Novel_Junctions.txt", - "rseqc_read_distribution_plot.txt", - "rseqc_read_dups.txt", - "rseqc_read_dups_plot.txt", - "salmon_plot.txt", - "samtools-flagstat-dp_Percentage_of_total.txt", - "samtools-flagstat-dp_Read_counts.txt", - "samtools-stats-dp.txt", - "samtools_alignment_plot.txt" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-26T19:01:52.559836" - }, - "hisat2/picard_metrics": { - "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", - "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", - "RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt", - "WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt", - "WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt" - 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"cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", + "deseq2.pca.vals.txt:md5,3f5285a2b412dbe7c1679b8a4c10b54a", + "deseq2.sample.dists.txt:md5,f9c7362a48c325a22e0b4027408c91b1", + "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", + "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", + "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", + "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", + "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", + "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", + "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", + "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c", + "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", + "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", + "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", + "fastqc_top_overrepresented_sequences_table-1.txt:md5,cf612406874da4e582eaeaa956f7eb66", + "fastqc_top_overrepresented_sequences_table.txt:md5,a415f85e91e40b3e33495c8966b589e6", + "flenDist.txt:md5,1868e7a2df81174ca588aafecd80c70b", + "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", + "flenDist.txt:md5,61e5e708c1821dd52f7bf27780cf3f40", + "flenDist.txt:md5,de061fb9c818d19e020ec922435a1701", + "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", + "hisat2_pe_plot.txt:md5,790eea3061c7b76d3a377f00b67c2d33", + "hisat2_se_plot.txt:md5,f8cd912353aa55e6e670b72a736b656c", + "junction_saturation_known.txt:md5,ba4cbbc75784e3e65fe33640602f521b", + "junction_saturation_novel.txt:md5,21ff86939339dd8266b53072e9460993", + "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", + "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", + "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", + "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", + "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", + "meta_info.json:md5,d309f5a801727c630feaedfe47e685f6", + "meta_info.json:md5,2ade91c056cdbcb37611b4b334446fa4", + "meta_info.json:md5,a1597f9f3c85dab21f3dacb5a44d5f86", + "meta_info.json:md5,9a81a81ae18c3de46e11e1b6904878bc", + "meta_info.json:md5,ae9ca7961887fd71eb7ab65d623ece14", + "multiqc_citations.txt:md5,da5043f8ab9b5bd51d91ccf3111c655e", + "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_dupradar-section-plot.txt:md5,1da98c781c8b4e1d5a7dfb754303fd40", + "multiqc_fail_strand_check_table.txt:md5,e978d026215cd23f0a22b08ab8d87903", + "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", + "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", + "multiqc_featurecounts_biotype_plot.txt:md5,d35ad008181f0f7be84d5770d17a3a65", + "multiqc_general_stats.txt:md5,9800d4f5f2f07358a8060bfeed0e83fb", + "multiqc_hisat2.txt:md5,8883842d3bca98a0b6651fcd0b3b8cca", + "multiqc_picard_dups.txt:md5,71d5bafee1a4916951349018f387f7a0", + "multiqc_rseqc_bam_stat.txt:md5,b259b4e713d5c1b11f61e5f4c2f24660", + "multiqc_rseqc_infer_experiment.txt:md5,4c095775f2212e68eaf957256cd410a3", + "multiqc_rseqc_junction_annotation.txt:md5,7576d6df2e66d72eebc0c2fb9f7fe56e", + "multiqc_rseqc_read_distribution.txt:md5,2254de1c5e6e726f085cb944e7a56442", + "multiqc_salmon.txt:md5,555f046898b8d65fa0a048587e05e70d", + "multiqc_salmon_deseq2_clustering-plot.txt:md5,eefa17f644cbf97076aba9cfbfedff4d", + "multiqc_salmon_deseq2_clustering-plot_1.txt:md5,a67da23bf2eeb579ace189f425c1bb2e", + "multiqc_salmon_deseq2_clustering-plot_2.txt:md5,593089606eefda4a9b57999f648537ce", + "multiqc_salmon_deseq2_clustering-plot_3.txt:md5,2fb3ec33fd1d13a4ce2f1f19c8b0e2e4", + "multiqc_salmon_deseq2_clustering-plot_4.txt:md5,a6dde4f32bba87777482e7c75844292e", + "multiqc_salmon_deseq2_pca-plot.txt:md5,fcd08e4ada29f1b4fe85792dba495325", + "multiqc_samtools_flagstat.txt:md5,e9f40853ae99749707c8d4114d3844ec", + "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49", + "multiqc_samtools_stats.txt:md5,d16b6c29fe344349ec7b2a3cecfe1c77", + "picard_deduplication.txt:md5,b54a144d4f23ade2221d7ca1af1997f4", + "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "qualimap_gene_coverage_profile_Counts.txt:md5,f3b9bb1902af4c7b5e04c0830ded2c02", + "qualimap_gene_coverage_profile_Normalised.txt:md5,ebcedec8e5c959414a4e89ccae3fc07e", + "qualimap_genomic_origin.txt:md5,dd514d2a42da9c4dd1ad4780aa4ac37e", + "qualimap_rnaseq_cov_hist.txt:md5,b78ff616f267f9b061b3297b767e88fb", + "qualimap_rnaseq_genome_results.txt:md5,44d4f08e147731faf8bcc6ace52f00f2", + "rnaseq_qc_results.txt:md5,2d7ef162c95fede85dca466bab3ba605", + "rnaseq_qc_results.txt:md5,200ad62a93ce4995af9ffe686c6cc1f4", + "rnaseq_qc_results.txt:md5,09508917659c8448598bf8b4f1a8f938", + "rnaseq_qc_results.txt:md5,5c981862809e2de3fdff9f9d20c43b38", + "rnaseq_qc_results.txt:md5,ccdc9ab548f2838505cd1f3301b9651d", + "rseqc_bam_stat.txt:md5,edfcffb5a74460da3870bec5522b2a3b", + "rseqc_infer_experiment_plot.txt:md5,0556a013129be7d78fac4345fddbe8c5", + "rseqc_inner_distance.txt:md5,47ce144d71786943ed7ce887d77d7b3e", + "rseqc_inner_distance_plot_Counts.txt:md5,aae91dacee2669231f0de5dc542addda", + "rseqc_inner_distance_plot_Percentages.txt:md5,e0b97b25e8629fdb5b936c584fa00661", + "rseqc_junction_annotation_junctions_plot_Events.txt:md5,db75ad02153035dea3ffaf58aa68894e", + "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,d233f89c3c69a0dfc2e66d4d5b8c7ea1", + "rseqc_junction_saturation_all.txt:md5,834981a3b3c2fb65e87883fb16c6a875", + "rseqc_junction_saturation_plot_All_Junctions.txt:md5,25467839fa2f94069ec67d3b46ddf7e9", + "rseqc_junction_saturation_plot_Known_Junctions.txt:md5,f18ba2fe3ab1a6b563aa4c4b11c5b0f8", + "rseqc_junction_saturation_plot_Novel_Junctions.txt:md5,35acb39867cae9e5e3df216f8e2af9a4", + "rseqc_read_distribution_plot.txt:md5,243e8358c7cb5a13d99f715c70c624cb", + "rseqc_read_dups.txt:md5,e79a116d76176f9e18532544a1f20ec4", + "rseqc_read_dups_plot.txt:md5,ed6a2aef667b65f49129c2af874fdbb5", + "salmon.merged.gene_counts.tsv:md5,c14cab7e15cfac73ec0602dc2c404551", + "salmon.merged.gene_counts_length_scaled.tsv:md5,b222b5c1faea3c464a1fe446cd4388ad", + "salmon.merged.gene_counts_scaled.tsv:md5,a210d2b06950b8d4ba1312509a028e18", + "salmon.merged.gene_lengths.tsv:md5,8f36e625921efbd23d0bcb57d353de9d", + "salmon.merged.gene_tpm.tsv:md5,dcd903f695d97a46d4b98215b48faeea", + "salmon.merged.transcript_counts.tsv:md5,ff0f5be09ca7a322672c0074ba35da17", + "salmon.merged.transcript_lengths.tsv:md5,81da7b0f0b61ee9ca23615d2c8b9a84e", + "salmon.merged.transcript_tpm.tsv:md5,b6986d60eaafcdacabca50d78e76f107", + "salmon_plot.txt:md5,59ee362906ef224982a20f32a2617c48", + "samtools-flagstat-dp_Percentage_of_total.txt:md5,edfac448e9dcd51f2bb11a84ca0c1be2", + "samtools-flagstat-dp_Read_counts.txt:md5,22647a049eebf1d595ebae3c67361ba1", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3625f666cc09d0f07990716aeccd869f", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,6c323b383a6506d124506405b9463d93", + "samtools-stats-dp.txt:md5,b50cdd0dfe9fedcdeb3f79477ef5180f", + "samtools_alignment_plot.txt:md5,b6ba3cc94a91b3d0a84c3fa721914744", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T13:40:29.820359" + "timestamp": "2024-09-13T11:23:27.694279" } } \ No newline at end of file diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index 7343798f7..0d8f63e93 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -15,176 +15,16 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name - ).match("bbsplit") }, - { assert snapshot( - path("${params.outdir}/custom/out/genome_gfp.fasta"), - path("${params.outdir}/custom/out/genome_gfp.gtf") - ).match("references") }, - { assert snapshot( - // HTMLs and ZIPs are not stable - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name - ).match("fastqc/trim") }, - { assert snapshot( - path("${params.outdir}/kallisto/tx2gene.tsv"), - // These files are not stable - file("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/abundance.h5").name, - file("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/abundance.tsv").name, - file("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/kallisto_quant.log").name, - file("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/run_info.json").name, - file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/abundance.h5").name, - file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/abundance.tsv").name, - file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/kallisto_quant.log").name, - file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/run_info.json").name, - file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/abundance.h5").name, - file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/abundance.tsv").name, - file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/kallisto_quant.log").name, - file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/run_info.json").name, - file("${params.outdir}/kallisto/WT_REP1/abundance.h5").name, - file("${params.outdir}/kallisto/WT_REP1/abundance.tsv").name, - file("${params.outdir}/kallisto/WT_REP1/kallisto_quant.log").name, - file("${params.outdir}/kallisto/WT_REP1/run_info.json").name, - file("${params.outdir}/kallisto/WT_REP2/abundance.h5").name, - file("${params.outdir}/kallisto/WT_REP2/abundance.tsv").name, - file("${params.outdir}/kallisto/WT_REP2/kallisto_quant.log").name, - file("${params.outdir}/kallisto/WT_REP2/run_info.json").name, - file("${params.outdir}/kallisto/kallisto.merged.gene_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/kallisto/kallisto.merged.gene_counts.tsv").name, - file("${params.outdir}/kallisto/kallisto.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/kallisto/kallisto.merged.gene_counts_length_scaled.tsv").name, - file("${params.outdir}/kallisto/kallisto.merged.gene_counts_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/kallisto/kallisto.merged.gene_counts_scaled.tsv").name, - file("${params.outdir}/kallisto/kallisto.merged.gene_lengths.tsv").name, - file("${params.outdir}/kallisto/kallisto.merged.gene_tpm.tsv").name, - file("${params.outdir}/kallisto/kallisto.merged.transcript_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/kallisto/kallisto.merged.transcript_counts.tsv").name, - file("${params.outdir}/kallisto/kallisto.merged.transcript_lengths.tsv").name, - file("${params.outdir}/kallisto/kallisto.merged.transcript_tpm.tsv").name - ).match("kallisto") }, - { assert snapshot( - path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc-status-check-heatmap.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_counts_plot.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/multiqc_citations.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/multiqc_cutadapt.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), - // These files are not stable - file("${params.outdir}/multiqc/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, - file("${params.outdir}/multiqc/multiqc_report_data/kallisto_alignment.txt").name, - file("${params.outdir}/multiqc/multiqc_report_data/multiqc_data.json").name, - file("${params.outdir}/multiqc/multiqc_report_data/multiqc_general_stats.txt").name, - file("${params.outdir}/multiqc/multiqc_report_data/multiqc_kallisto.txt").name, - file("${params.outdir}/multiqc/multiqc_report_data/multiqc_software_versions.txt").name, - file("${params.outdir}/multiqc/multiqc_report_data/multiqc_sources.txt").name - ).match("multiqc_data") }, + { assert workflow.success}, { assert snapshot( - path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), - // PDFs, SVGs, some PNGs and HTML reports are not stable - file("${params.outdir}/multiqc/multiqc_report.html").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/general_stats_table.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/kallisto_alignment-cnt.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/kallisto_alignment-pct.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, - file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, - file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, - file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, - file("${params.outdir}/multiqc/multiqc_report_plots/png/general_stats_table.png").name, - file("${params.outdir}/multiqc/multiqc_report_plots/png/kallisto_alignment-cnt.png").name, - file("${params.outdir}/multiqc/multiqc_report_plots/png/kallisto_alignment-pct.png").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/general_stats_table.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/kallisto_alignment-cnt.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/kallisto_alignment-pct.svg").name - ).match("multiqc_plots") }, - { assert snapshot( - // These reports are not stable - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name - ).match("trimgalore") }, - { assert snapshot( - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") - ).match("versions") } + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file_complement.collect { it.getName() }, + snapshottable_files + ).match() } ) } } @@ -203,21 +43,15 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, + { assert workflow.success}, { assert snapshot( UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, - file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, - file("${params.outdir}/multiqc/multiqc_report.html").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + file_complement.collect { it.getName() }, + snapshottable_files ).match() } ) } diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index a431f33fc..ceffc6ab0 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -1,241 +1,370 @@ { - "multiqc_data": { + "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment": { "content": [ - "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", - "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", - "fastqc-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", - "fastqc_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", - "fastqc_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", - "fastqc_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c", - "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", - "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "fastqc_top_overrepresented_sequences_table.txt", - "kallisto_alignment.txt", - "multiqc_data.json", - "multiqc_general_stats.txt", - "multiqc_kallisto.txt", - "multiqc_software_versions.txt", - "multiqc_sources.txt" + { + "BBMAP_BBSPLIT": { + "bbmap": 39.01 + }, + "CAT_FASTQ": { + "cat": 8.3 + }, + "CUSTOM_CATADDITIONALFASTA": { + "python": "3.9.5" + }, + "CUSTOM_GETCHROMSIZES": { + "getchromsizes": 1.2 + }, + "CUSTOM_TX2GENE": { + "python": "3.9.5" + }, + "FQ_SUBSAMPLE": { + "fq": "0.9.1 (2022-02-22)" + }, + "GTF2BED": { + "perl": "5.26.2" + }, + "GTF_FILTER": { + "python": "3.9.5" + }, + "GUNZIP_ADDITIONAL_FASTA": { + "gunzip": 1.1 + }, + "GUNZIP_GTF": { + "gunzip": 1.1 + }, + "KALLISTO_INDEX": { + "kallisto": "0.48.0" + }, + "KALLISTO_QUANT": { + "kallisto": "0.48.0" + }, + "SALMON_QUANT": { + "salmon": "1.10.1" + }, + "SE_GENE": { + "bioconductor-summarizedexperiment": "1.32.0" + }, + "TRIMGALORE": { + "trimgalore": "0.6.7", + "cutadapt": 3.4 + }, + "TXIMETA_TXIMPORT": { + "bioconductor-tximeta": "1.20.1" + }, + "UNTAR_SALMON_INDEX": { + "untar": 1.34 + }, + "Workflow": { + "nf-core/rnaseq": "v3.16.0dev" + } + }, + [ + "RAP1_IAA_30M_REP1", + "RAP1_IAA_30M_REP1.stats.txt", + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "RAP1_UNINDUCED_REP1", + "RAP1_UNINDUCED_REP1.stats.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "RAP1_UNINDUCED_REP2", + "RAP1_UNINDUCED_REP2.stats.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "WT_REP1", + "WT_REP1.stats.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1_val_1_fastqc.html", + "WT_REP1_trimmed_1_val_1_fastqc.zip", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2_val_2_fastqc.html", + "WT_REP1_trimmed_2_val_2_fastqc.zip", + "WT_REP2", + "WT_REP2.stats.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1_val_1_fastqc.html", + "WT_REP2_trimmed_1_val_1_fastqc.zip", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2_val_2_fastqc.html", + "WT_REP2_trimmed_2_val_2_fastqc.zip", + "abundance.h5", + "abundance.h5", + "abundance.h5", + "abundance.h5", + "abundance.h5", + "abundance.tsv", + "abundance.tsv", + "abundance.tsv", + "abundance.tsv", + "abundance.tsv", + "bbsplit", + "custom", + "cutadapt_filtered_reads_plot-cnt.pdf", + "cutadapt_filtered_reads_plot-cnt.png", + "cutadapt_filtered_reads_plot-cnt.svg", + "cutadapt_filtered_reads_plot-pct.pdf", + "cutadapt_filtered_reads_plot-pct.png", + "cutadapt_filtered_reads_plot-pct.svg", + "cutadapt_filtered_reads_plot.txt", + "cutadapt_trimmed_sequences_plot_3_Counts.pdf", + "cutadapt_trimmed_sequences_plot_3_Counts.png", + "cutadapt_trimmed_sequences_plot_3_Counts.svg", + "cutadapt_trimmed_sequences_plot_3_Counts.txt", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "fastqc", + "fastqc-status-check-heatmap.pdf", + "fastqc-status-check-heatmap.png", + "fastqc-status-check-heatmap.svg", + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.pdf", + "fastqc_top_overrepresented_sequences_table.png", + "fastqc_top_overrepresented_sequences_table.svg", + "fastqc_top_overrepresented_sequences_table.txt", + "general_stats_table.pdf", + "general_stats_table.png", + "general_stats_table.svg", + "genome_gfp.fasta", + "genome_gfp.gtf", + "kallisto", + "kallisto.merged.gene_counts.SummarizedExperiment.rds", + "kallisto.merged.gene_counts.tsv", + "kallisto.merged.gene_counts_length_scaled.SummarizedExperiment.rds", + "kallisto.merged.gene_counts_length_scaled.tsv", + "kallisto.merged.gene_counts_scaled.SummarizedExperiment.rds", + "kallisto.merged.gene_counts_scaled.tsv", + "kallisto.merged.gene_lengths.tsv", + "kallisto.merged.gene_tpm.tsv", + "kallisto.merged.transcript_counts.SummarizedExperiment.rds", + "kallisto.merged.transcript_counts.tsv", + "kallisto.merged.transcript_lengths.tsv", + "kallisto.merged.transcript_tpm.tsv", + "kallisto_alignment-cnt.pdf", + "kallisto_alignment-cnt.png", + "kallisto_alignment-cnt.svg", + "kallisto_alignment-pct.pdf", + "kallisto_alignment-pct.png", + "kallisto_alignment-pct.svg", + 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"WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt", + "custom", + "fastqc", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", + "multiqc", + "multiqc_data", + "multiqc_plots", + "multiqc_report.html", + "nf_core_rnaseq_software_mqc_versions.yml", + "out", + "pipeline_info", + "trim", + "trimgalore" + ], + [ + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:36:19.174739" + "timestamp": "2024-09-13T11:28:04.202471" } } \ No newline at end of file diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index b5110dbf2..131b0f0a0 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -1,11 +1,50 @@ -// Function to remove Nextflow version from pipeline_software_mqc_versions.yml - class UTILS { + // Remove Nextflow version from pipeline_software_mqc_versions.yml public static Object removeNextflowVersion(pipeline_software_mqc_versions) { def softwareVersions = path(pipeline_software_mqc_versions).yaml - if (softwareVersions.containsKey("Workflow")) { - softwareVersions.Workflow.remove("Nextflow") - } + if (softwareVersions.containsKey("Workflow")) softwareVersions.Workflow.remove("Nextflow") return softwareVersions } + + // Recursively list all files in a directory and its sub-directories, matching or not matching supplied suffixes + public static getAllFilesFromDir(dir, List includeRegexes = null, List excludeRegexes = null) { + def output = [] + new File(dir).eachFileRecurse() { file -> + boolean matchesInclusion = (includeRegexes == null || includeRegexes.any { regex -> file.name.toString() ==~ regex }) + boolean matchesExclusion = (excludeRegexes == null || !excludeRegexes.any { regex -> file.name.toString() ==~ regex }) + + // Conditionally add either full path or just the file name + if (matchesInclusion && matchesExclusion) { + output.add(file) + } + } + return output.sort { it.name } + } + + // Static (global) exclusion regexes list + static List exclusionRegexesForUnstableFileNames = [/.*\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}.*/] + static List snapshottablePatterns = [/.*\.(txt|json|tsv)$/] + static List exclusionRegexesForUnstableFileContents = [ + // To exclude files with timestamps in the format YYYY-MM-DD_HH-MM-SS + /\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}/, + // To exclude "goleft_indexcov-bin-plot.txt" + /goleft_indexcov-bin-plot\.txt/, + // To exclude "multiqc_data.json" + /multiqc_data\.json/, + // To exclude "multiqc_sources.txt" + /multiqc_sources\.txt/, + // To exclude params files with timestamps + /params_\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}\.json/, + // To exclude "*.deduped.cram.metrics.multiqc.tsv" + /.*\.deduped\.cram\.metrics\.multiqc\.tsv/, + // To exclude "goleft_bin.txt" + /goleft_bin\.txt/, + // To exclude "goleft_roc.txt" + /goleft_roc\.txt/, + // To exclude any "multiqc_sample*.txt" files + /multiqc_sample.*\.txt/, + // To exclude "multiqc_software_versions.txt" + /multiqc_software_versions\.txt/ + ] + } diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index dde1c3706..c1622036f 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -13,797 +13,16 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name - ).match("bbsplit") }, - { assert snapshot( - path("${params.outdir}/custom/out/genome_gfp.fasta"), - path("${params.outdir}/custom/out/genome_gfp.gtf") - ).match("references") }, - { assert snapshot( - // HTMLs and ZIPs are not stable - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name - ).match("fastqc/raw") }, - { assert snapshot( - // HTMLs and ZIPs are not stable - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name - ).match("fastqc/trim") }, - { assert snapshot( - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_mapped_samples_table.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), - // These files are not stable - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name - ).match("multiqc_data") }, - { assert snapshot( - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_mapped_samples_table.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), - // PDFs, SVGs, some PNGs and HTML reports are not stable - file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_mapped_samples_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, - 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file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_bam_stat.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name - ).match("multiqc_plots") }, - { assert snapshot( - path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"), - // These files are not stable - file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name - ).match("salmon/deseq2_qc") }, - { assert snapshot( - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), - // These files are not stable - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP1/quant.sf").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP2/quant.sf").name - ).match("salmon_quant") }, - { assert snapshot( - path("${params.outdir}/salmon/tx2gene.tsv"), - // These files are not stable - file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name - ).match("salmon") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name - ).match("star_salmon/bigwig") }, - { assert snapshot( - path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), - // These files are not stable - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt").name - ).match("star_salmon/deseq2_qc") }, - { assert snapshot( - path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"), - // PDFs are not stable - file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name - ).match("star_salmon/dupradar") }, - { assert snapshot( - path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"), - file("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name, - file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name, - file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name - ).match("star_salmon/featurecounts") }, + { assert workflow.success}, { assert snapshot( - path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"), - // Logs are not stable - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name - ).match("star_salmon/log") }, - { assert snapshot( - // Metrics are not stable - file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name - ).match("star_salmon/picard_metrics") }, - { assert snapshot( - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - // HTML reports and these files are not stable - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name - ).match("star_salmon/qualimap") }, - { assert snapshot( - path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), - // PDFs, R scripts and all these files are not stable - file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name - ).match("star_salmon/rseqc") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name - ).match("star_salmon/salmon") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name - ).match("star_salmon/samtools_stats") }, - { assert snapshot( - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"), - // These files are not stable - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name - ).match("star_salmon/stringtie") }, - { assert snapshot( - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name - ).match("star_salmon/markdup") }, - { assert snapshot( - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"), - path("${params.outdir}/star_salmon/tx2gene.tsv"), - // These files are not stable - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name, - file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name, - file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name - ).match("star_salmon/salmon_quant") }, - { assert snapshot( - // These reports are not stable - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name - ).match("trimgalore") }, - { assert snapshot( - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") - ).match("versions") } + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file_complement.collect { it.getName() }, + snapshottable_files + ).match() } ) } } @@ -820,31 +39,15 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, + { assert workflow.success}, { assert snapshot( UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, - file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + file_complement.collect { it.getName() }, + snapshottable_files ).match() } ) } diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index c68828368..4aa9488c4 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -1,970 +1,1374 @@ { - "star_salmon/log": { + "Params: --min_mapped_reads 90": { "content": [ - "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", - "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", - "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", - "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204", - "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23", - "RAP1_IAA_30M_REP1.Log.final.out", - "RAP1_IAA_30M_REP1.Log.out", - "RAP1_IAA_30M_REP1.Log.progress.out", - "RAP1_UNINDUCED_REP1.Log.final.out", - "RAP1_UNINDUCED_REP1.Log.out", - "RAP1_UNINDUCED_REP1.Log.progress.out", - "RAP1_UNINDUCED_REP2.Log.final.out", - "RAP1_UNINDUCED_REP2.Log.out", - "RAP1_UNINDUCED_REP2.Log.progress.out", - "WT_REP1.Log.final.out", - "WT_REP1.Log.out", - "WT_REP1.Log.progress.out", - "WT_REP2.Log.final.out", - "WT_REP2.Log.out", - "WT_REP2.Log.progress.out" + { + "BBMAP_BBSPLIT": { + "bbmap": 39.01 + }, + "BEDTOOLS_GENOMECOV_FW": { + "bedtools": "2.31.1" + }, + "CAT_FASTQ": { + "cat": 8.3 + }, + "CUSTOM_CATADDITIONALFASTA": { + "python": "3.9.5" + }, + "CUSTOM_GETCHROMSIZES": { + "getchromsizes": 1.2 + }, + "CUSTOM_TX2GENE": { + "python": "3.9.5" + }, + "DESEQ2_QC_PSEUDO": { + "r-base": "4.0.3", + "bioconductor-deseq2": "1.28.0" + }, + "DESEQ2_QC_STAR_SALMON": { + "r-base": "4.0.3", + "bioconductor-deseq2": "1.28.0" + }, + "DUPRADAR": { + "bioconductor-dupradar": "1.32.0" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "FQ_SUBSAMPLE": { + "fq": "0.9.1 (2022-02-22)" + }, + "GTF2BED": { + "perl": "5.26.2" + }, + "GTF_FILTER": { + "python": "3.9.5" + }, + "GUNZIP_ADDITIONAL_FASTA": { + "gunzip": 1.1 + }, + "GUNZIP_GTF": { + "gunzip": 1.1 + }, + "MULTIQC_CUSTOM_BIOTYPE": { + "python": "3.9.5" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.1.1" + }, + "QUALIMAP_RNASEQ": { + "qualimap": 2.3 + }, + "RSEQC_BAMSTAT": { + "rseqc": "5.0.2" + }, + "RSEQC_INFEREXPERIMENT": { + "rseqc": "5.0.2" + }, + "RSEQC_INNERDISTANCE": { + "rseqc": "5.0.2" + }, + "RSEQC_JUNCTIONANNOTATION": { + "rseqc": "5.0.2" + }, + "RSEQC_JUNCTIONSATURATION": { + "rseqc": "5.0.2" + }, + "RSEQC_READDISTRIBUTION": { + "rseqc": "5.0.2" + }, + "RSEQC_READDUPLICATION": { + "rseqc": "5.0.2" + }, + "SALMON_QUANT": { + "salmon": "1.10.1" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": 1.2 + }, + "SAMTOOLS_IDXSTATS": { + "samtools": 1.2 + }, + "SAMTOOLS_INDEX": { + "samtools": 1.2 + }, + "SAMTOOLS_SORT": { + "samtools": 1.2 + }, + "SAMTOOLS_STATS": { + "samtools": 1.2 + }, + "SE_GENE": { + "bioconductor-summarizedexperiment": "1.32.0" + }, + "STAR_ALIGN": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "STAR_GENOMEGENERATE": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "STRINGTIE_STRINGTIE": { + "stringtie": "2.2.1" + }, + "SUBREAD_FEATURECOUNTS": { + "subread": "2.0.1" + }, + "TRIMGALORE": { + "trimgalore": "0.6.7", + "cutadapt": 3.4 + }, + "TXIMETA_TXIMPORT": { + "bioconductor-tximeta": "1.20.1" + }, + "UCSC_BEDCLIP": { + "ucsc": 377 + }, + "UCSC_BEDGRAPHTOBIGWIG": { + "ucsc": 445 + }, + "UNTAR_SALMON_INDEX": { + "untar": 1.34 + }, + "Workflow": { + "nf-core/rnaseq": "v3.16.0dev" + } + }, + [ + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", + "Coverage Profile Along Genes (Total).png", + "Coverage Profile Along Genes (Total).png", + "Junction Analysis.png", + "Junction Analysis.png", + "Junction Analysis.png", + "RAP1_IAA_30M_REP1", + "RAP1_IAA_30M_REP1", + "RAP1_IAA_30M_REP1", + "RAP1_IAA_30M_REP1.DupRate_plot.pdf", + "RAP1_IAA_30M_REP1.DupRate_plot.r", + "RAP1_IAA_30M_REP1.Log.final.out", + "RAP1_IAA_30M_REP1.Log.out", + "RAP1_IAA_30M_REP1.Log.progress.out", + "RAP1_IAA_30M_REP1.SJ.out.tab", + "RAP1_IAA_30M_REP1.ballgown", + "RAP1_IAA_30M_REP1.bam_stat.txt", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv", + "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv", + "RAP1_IAA_30M_REP1.coverage.gtf", + "RAP1_IAA_30M_REP1.featureCounts.txt", + "RAP1_IAA_30M_REP1.featureCounts.txt.summary", + "RAP1_IAA_30M_REP1.forward.bigWig", + "RAP1_IAA_30M_REP1.gene.abundance.txt", + "RAP1_IAA_30M_REP1.infer_experiment.txt", + "RAP1_IAA_30M_REP1.inner_distance.txt", + "RAP1_IAA_30M_REP1.inner_distance_freq.txt", + "RAP1_IAA_30M_REP1.inner_distance_mean.txt", + "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", + "RAP1_IAA_30M_REP1.inner_distance_plot.r", + "RAP1_IAA_30M_REP1.junction.Interact.bed", + "RAP1_IAA_30M_REP1.junction.bed", + "RAP1_IAA_30M_REP1.junction.xls", + "RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf", + "RAP1_IAA_30M_REP1.junctionSaturation_plot.r", + "RAP1_IAA_30M_REP1.junction_annotation.log", + "RAP1_IAA_30M_REP1.junction_plot.r", + "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", + "RAP1_IAA_30M_REP1.markdup.sorted.bam", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.pos.DupRate.xls", + "RAP1_IAA_30M_REP1.read_distribution.txt", + "RAP1_IAA_30M_REP1.reverse.bigWig", + "RAP1_IAA_30M_REP1.seq.DupRate.xls", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", + "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_IAA_30M_REP1.splice_events.pdf", + "RAP1_IAA_30M_REP1.splice_junction.pdf", + "RAP1_IAA_30M_REP1.stats.txt", + "RAP1_IAA_30M_REP1.transcripts.gtf", + "RAP1_IAA_30M_REP1.txt", + "RAP1_IAA_30M_REP1.txt", + "RAP1_IAA_30M_REP1_dupMatrix.txt", + "RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf", + "RAP1_IAA_30M_REP1_duprateExpDens.pdf", + "RAP1_IAA_30M_REP1_expressionHist.pdf", + "RAP1_IAA_30M_REP1_intercept_slope.txt", + "RAP1_IAA_30M_REP1_raw_1_fastqc.html", + "RAP1_IAA_30M_REP1_raw_1_fastqc.zip", + "RAP1_IAA_30M_REP1_raw_2_fastqc.html", + "RAP1_IAA_30M_REP1_raw_2_fastqc.zip", + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "RAP1_UNINDUCED_REP1", + "RAP1_UNINDUCED_REP1", + "RAP1_UNINDUCED_REP1", + "RAP1_UNINDUCED_REP1.DupRate_plot.pdf", + "RAP1_UNINDUCED_REP1.DupRate_plot.r", + "RAP1_UNINDUCED_REP1.Log.final.out", + "RAP1_UNINDUCED_REP1.Log.out", + "RAP1_UNINDUCED_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP1.SJ.out.tab", + "RAP1_UNINDUCED_REP1.ballgown", + "RAP1_UNINDUCED_REP1.bam_stat.txt", + "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv", + "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv", + "RAP1_UNINDUCED_REP1.coverage.gtf", + "RAP1_UNINDUCED_REP1.featureCounts.txt", + "RAP1_UNINDUCED_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP1.forward.bigWig", + "RAP1_UNINDUCED_REP1.gene.abundance.txt", + "RAP1_UNINDUCED_REP1.infer_experiment.txt", + "RAP1_UNINDUCED_REP1.junction.Interact.bed", + "RAP1_UNINDUCED_REP1.junction.bed", + "RAP1_UNINDUCED_REP1.junction.xls", + "RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf", + "RAP1_UNINDUCED_REP1.junctionSaturation_plot.r", + "RAP1_UNINDUCED_REP1.junction_annotation.log", + "RAP1_UNINDUCED_REP1.junction_plot.r", + "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", + 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"RAP1_UNINDUCED_REP2.forward.bigWig", - "RAP1_UNINDUCED_REP2.reverse.bigWig" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T16:20:15.635275" - }, - "versions": { - "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T16:36:12.954252" - }, - "fastqc/trim": { - "content": [ - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", - "WT_REP1_trimmed_1_val_1_fastqc.html", - "WT_REP1_trimmed_1_val_1_fastqc.zip", - "WT_REP1_trimmed_2_val_2_fastqc.html", - "WT_REP1_trimmed_2_val_2_fastqc.zip", - "WT_REP2_trimmed_1_val_1_fastqc.html", - "WT_REP2_trimmed_1_val_1_fastqc.zip", - "WT_REP2_trimmed_2_val_2_fastqc.html", - "WT_REP2_trimmed_2_val_2_fastqc.zip" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T16:04:54.759052" - }, - "star_salmon/dupradar": { - "content": [ - "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", - "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", - "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", - "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79", - "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b", - "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043", - "RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf", - "RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf", - "RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf", - "RAP1_IAA_30M_REP1_expressionHist.pdf", - "RAP1_UNINDUCED_REP1_expressionHist.pdf", - "RAP1_UNINDUCED_REP2_expressionHist.pdf", - "RAP1_IAA_30M_REP1_duprateExpDens.pdf", - "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", - "RAP1_UNINDUCED_REP2_duprateExpDens.pdf" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T16:36:12.202189" - }, - "bbsplit": { - "content": [ - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T16:04:54.719906" - }, - "star_salmon/qualimap": { - "content": [ - "Coverage Profile Along Genes (High).png:md5,876c1b88f33bd3e5fe1a41679729573d", - "Coverage Profile Along Genes (Low).png:md5,ee1f2c9cc4dd4867811eda1e68864ab4", - "Coverage Profile Along Genes (Total).png:md5,53747a8f9813744902756ad60638380a", - "Transcript coverage histogram.png:md5,4f9072d4b11216373b59396293803a37", - "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8", - "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", - "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", - "Coverage Profile Along Genes (High).png:md5,bbf0531018e7fccfc1dfdd1c05715518", - "Coverage Profile Along Genes (Low).png:md5,3c147d9c831d4be98615a22a72fad05d", - "Coverage Profile Along Genes (Total).png:md5,5a8a6db3a8d19a2dcb8f715b11e67c50", - "Transcript coverage histogram.png:md5,488440d7b6d73bcd4567316712e281fe", - "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3", - "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff", - "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff", - "Coverage Profile Along Genes (High).png:md5,5a5d99cc7a1dba3762d67f4aa4adad58", - "Coverage Profile Along Genes (Low).png:md5,b6adc296e9a732aa0495a6da8fa4ed90", - "Coverage Profile Along Genes (Total).png:md5,fcb94fb9c1a51c1db32f884d05929cc8", - "Transcript coverage histogram.png:md5,3aeb52ff3e3752727a370b0d7ceb0518", - "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", - "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d", - "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d", - "Junction Analysis.png", - "Reads Genomic Origin.png", - "qualimapReport.html", - "rnaseq_qc_results.txt", - "Junction Analysis.png", - "Reads Genomic Origin.png", - "qualimapReport.html", - "rnaseq_qc_results.txt", - "Junction Analysis.png", - "Reads Genomic Origin.png", - "qualimapReport.html", - "rnaseq_qc_results.txt" + { + "BBMAP_BBSPLIT": { + "bbmap": 39.01 + }, + "CAT_FASTQ": { + "cat": 8.3 + }, + "CUSTOM_CATADDITIONALFASTA": { + "python": null + }, + "CUSTOM_GETCHROMSIZES": { + "getchromsizes": 1.2 + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GTF2BED": { + "perl": "5.26.2" + }, + "GTF_FILTER": { + "python": "3.9.5" + }, + "GUNZIP_ADDITIONAL_FASTA": { + "gunzip": 1.1 + }, + "GUNZIP_GTF": { + "gunzip": 1.1 + }, + "STAR_GENOMEGENERATE": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "TRIMGALORE": { + "trimgalore": "0.6.7", + "cutadapt": 3.4 + }, + "UNTAR_SALMON_INDEX": { + "untar": 1.34 + }, + "Workflow": { + "nf-core/rnaseq": "v3.16.0dev" + } + }, + [ + "RAP1_IAA_30M_REP1_raw.html", + "RAP1_IAA_30M_REP1_raw.zip", + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_raw.html", + "RAP1_UNINDUCED_REP1_raw.zip", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_raw.html", + "RAP1_UNINDUCED_REP2_raw.zip", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_raw.html", + "WT_REP1_raw.zip", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_raw.html", + "WT_REP2_raw.zip", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt", + "custom", + "fastqc", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", + "multiqc", + "multiqc_data", + "multiqc_plots", + "multiqc_report.html", + "nf_core_rnaseq_software_mqc_versions.yml", + "out", + "pipeline_info", + "raw", + "star_salmon", + "trim", + "trimgalore" + ], + [ + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T13:06:37.041504" + "timestamp": "2024-09-13T11:36:05.962174" } } \ No newline at end of file diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index 430f18b6f..c0cb4f24e 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -13,923 +13,16 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name - ).match("bbsplit") }, - { assert snapshot( - path("${params.outdir}/custom/out/genome_gfp.fasta"), - path("${params.outdir}/custom/out/genome_gfp.gtf") - ).match("references") }, - { assert snapshot( - // HTMLs and ZIPs are not stable - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name - ).match("fastqc/raw") }, - { assert snapshot( - // HTMLs and ZIPs are not stable - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name - ).match("fastqc/trim") }, - { assert snapshot( - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), - // These files are not stable - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sortmerna.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/sortmerna-detailed-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name - ).match("multiqc_data") }, - { assert snapshot( - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/sortmerna-detailed-plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/sortmerna-detailed-plot-pct.png"), - // PDFs, SVGs, some PNGs and HTML reports are not stable - file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/sortmerna-detailed-plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/sortmerna-detailed-plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_bam_stat.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/sortmerna-detailed-plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/sortmerna-detailed-plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name - ).match("multiqc_plots") }, - { assert snapshot( - path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"), - // These files are not stable - file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name - ).match("salmon/deseq2_qc") }, - { assert snapshot( - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), - // These files are not stable - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP1/quant.sf").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP2/quant.sf").name - ).match("salmon_quant") }, - { assert snapshot( - path("${params.outdir}/salmon/tx2gene.tsv"), - // These files are not stable - file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name - ).match("salmon") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/sortmerna/RAP1_IAA_30M_REP1.sortmerna.log").name, - file("${params.outdir}/sortmerna/RAP1_UNINDUCED_REP1.sortmerna.log").name, - file("${params.outdir}/sortmerna/RAP1_UNINDUCED_REP2.sortmerna.log").name, - file("${params.outdir}/sortmerna/WT_REP1.sortmerna.log").name, - file("${params.outdir}/sortmerna/WT_REP2.sortmerna.log").name - ).match("star_salmon/sortmerna") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig").name - ).match("star_salmon/bigwig") }, - { assert snapshot( - path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), - // These files are not stable - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt").name - ).match("star_salmon/deseq2_qc") }, - { assert snapshot( - path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP1_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP2_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"), - // PDFs are not stable - file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP1_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP2_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name - ).match("star_salmon/dupradar") }, + { assert workflow.success}, { assert snapshot( - path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt"), - file("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name, - file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name, - file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name, - file("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt.summary").name, - file("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt.summary").name - ).match("star_salmon/featurecounts") }, - { assert snapshot( - path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"), - // Logs are not stable - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name - ).match("star_salmon/log") }, - { assert snapshot( - // Metrics are not stable - file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name - ).match("star_salmon/picard_metrics") }, - { assert snapshot( - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - // HTML reports and these files are not stable - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt").name - ).match("star_salmon/qualimap") }, - { assert snapshot( - path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), - // PDFs, R scripts and all these files are not stable - file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name - ).match("star_salmon/rseqc") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name - ).match("star_salmon/salmon") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name - ).match("star_salmon/samtools_stats") }, - { assert snapshot( - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab"), - // These files are not stable - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf").name - ).match("star_salmon/stringtie") }, - { assert snapshot( - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name - ).match("star_salmon/markdup") }, - { assert snapshot( - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"), - path("${params.outdir}/star_salmon/tx2gene.tsv"), - // These files are not stable - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name, - file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name, - file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name - ).match("star_salmon/salmon_quant") }, - { assert snapshot( - // These reports are not stable - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name - ).match("trimgalore") }, - { assert snapshot( - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") - ).match("versions") } + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file_complement.collect { it.getName() }, + snapshottable_files + ).match() } ) } } @@ -946,31 +39,15 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, + { assert workflow.success}, { assert snapshot( UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, - file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + file_complement.collect { it.getName() }, + snapshottable_files ).match() } ) } diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index a6e841b08..ab3b51ac9 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -1,1102 +1,1598 @@ { - "star_salmon/log": { + "Params: --remove_ribo_rna": { "content": [ - "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", - "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", - "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", - "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204", - "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23", - "RAP1_IAA_30M_REP1.Log.final.out", - "RAP1_IAA_30M_REP1.Log.out", - "RAP1_IAA_30M_REP1.Log.progress.out", - "RAP1_UNINDUCED_REP1.Log.final.out", - "RAP1_UNINDUCED_REP1.Log.out", - "RAP1_UNINDUCED_REP1.Log.progress.out", - "RAP1_UNINDUCED_REP2.Log.final.out", - "RAP1_UNINDUCED_REP2.Log.out", - "RAP1_UNINDUCED_REP2.Log.progress.out", - "WT_REP1.Log.final.out", - "WT_REP1.Log.out", - "WT_REP1.Log.progress.out", - "WT_REP2.Log.final.out", - "WT_REP2.Log.out", - "WT_REP2.Log.progress.out" + { + "BBMAP_BBSPLIT": { + "bbmap": 39.01 + }, + "BEDTOOLS_GENOMECOV_FW": { + "bedtools": "2.31.1" + }, + "CAT_FASTQ": { + "cat": 8.3 + }, + "CUSTOM_CATADDITIONALFASTA": { + "python": "3.9.5" + }, + "CUSTOM_GETCHROMSIZES": { + "getchromsizes": 1.2 + }, + "CUSTOM_TX2GENE": { + "python": "3.9.5" + }, + "DESEQ2_QC_PSEUDO": { + "r-base": "4.0.3", + "bioconductor-deseq2": "1.28.0" + }, + "DESEQ2_QC_STAR_SALMON": { + "r-base": "4.0.3", + "bioconductor-deseq2": "1.28.0" + }, + "DUPRADAR": { + "bioconductor-dupradar": "1.32.0" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "FQ_SUBSAMPLE": { + "fq": "0.9.1 (2022-02-22)" + }, + "GTF2BED": { + "perl": "5.26.2" + }, + "GTF_FILTER": { + "python": "3.9.5" + }, + "GUNZIP_ADDITIONAL_FASTA": { + "gunzip": 1.1 + }, + "GUNZIP_GTF": { + "gunzip": 1.1 + }, + "MULTIQC_CUSTOM_BIOTYPE": { + "python": "3.9.5" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.1.1" + }, + "QUALIMAP_RNASEQ": { + "qualimap": 2.3 + }, + "RSEQC_BAMSTAT": { + "rseqc": "5.0.2" + }, + "RSEQC_INFEREXPERIMENT": { + "rseqc": "5.0.2" + }, + "RSEQC_INNERDISTANCE": { + "rseqc": "5.0.2" + }, + "RSEQC_JUNCTIONANNOTATION": { + "rseqc": "5.0.2" + }, + "RSEQC_JUNCTIONSATURATION": { + "rseqc": "5.0.2" + }, + "RSEQC_READDISTRIBUTION": { + "rseqc": "5.0.2" + }, + "RSEQC_READDUPLICATION": { + "rseqc": "5.0.2" + }, + "SALMON_QUANT": { + "salmon": "1.10.1" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": 1.2 + }, + "SAMTOOLS_IDXSTATS": { + "samtools": 1.2 + }, + "SAMTOOLS_INDEX": { + "samtools": 1.2 + }, + "SAMTOOLS_SORT": { + "samtools": 1.2 + }, + "SAMTOOLS_STATS": { + "samtools": 1.2 + }, + "SE_GENE": { + "bioconductor-summarizedexperiment": "1.32.0" + }, + "SORTMERNA": { + "sortmerna": "4.3.6" + }, + "SORTMERNA_INDEX": { + "sortmerna": "4.3.6" + }, + "STAR_ALIGN": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "STAR_GENOMEGENERATE": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "STRINGTIE_STRINGTIE": { + "stringtie": "2.2.1" + }, + "SUBREAD_FEATURECOUNTS": { + "subread": "2.0.1" + }, + "TRIMGALORE": { + "trimgalore": "0.6.7", + "cutadapt": 3.4 + }, + "TXIMETA_TXIMPORT": { + "bioconductor-tximeta": "1.20.1" + }, + "UCSC_BEDCLIP": { + "ucsc": 377 + }, + "UCSC_BEDGRAPHTOBIGWIG": { + "ucsc": 445 + }, + "UNTAR_SALMON_INDEX": { + "untar": 1.34 + }, + "Workflow": { + "nf-core/rnaseq": "v3.16.0dev" + } + }, + [ + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", + "Coverage Profile Along Genes (Total).png", + "Coverage Profile Along Genes (Total).png", + "Coverage Profile Along Genes (Total).png", + "Coverage Profile Along Genes (Total).png", + "Junction Analysis.png", + "Junction Analysis.png", + "Junction Analysis.png", + "Junction Analysis.png", + "Junction Analysis.png", + "RAP1_IAA_30M_REP1", + "RAP1_IAA_30M_REP1", + "RAP1_IAA_30M_REP1", + "RAP1_IAA_30M_REP1.DupRate_plot.pdf", + 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"salmon.merged.gene_counts_length_scaled.tsv", - "salmon.merged.gene_counts_scaled.SummarizedExperiment.rds", - "salmon.merged.gene_counts_scaled.tsv", - "salmon.merged.gene_lengths.tsv", - "salmon.merged.gene_tpm.tsv", - "salmon.merged.transcript_counts.SummarizedExperiment.rds", - "salmon.merged.transcript_counts.tsv", - "salmon.merged.transcript_lengths.tsv", - "salmon.merged.transcript_tpm.tsv" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T18:00:13.112566" - }, - "star_salmon/bigwig": { - "content": [ - "RAP1_IAA_30M_REP1.forward.bigWig", - "RAP1_IAA_30M_REP1.reverse.bigWig", - "RAP1_UNINDUCED_REP1.forward.bigWig", - "RAP1_UNINDUCED_REP1.reverse.bigWig", - "RAP1_UNINDUCED_REP2.forward.bigWig", - "RAP1_UNINDUCED_REP2.reverse.bigWig", - "WT_REP1.forward.bigWig", - "WT_REP1.reverse.bigWig", - "WT_REP2.forward.bigWig", - "WT_REP2.reverse.bigWig" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T18:18:52.080654" - }, - "star_salmon/sortmerna": { - "content": [ - "RAP1_IAA_30M_REP1.sortmerna.log", - "RAP1_UNINDUCED_REP1.sortmerna.log", - "RAP1_UNINDUCED_REP2.sortmerna.log", - "WT_REP1.sortmerna.log", - "WT_REP2.sortmerna.log" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T18:18:51.881667" - }, - "versions": { - "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, SORTMERNA={sortmerna=4.3.6}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T18:00:14.01652" - }, - "fastqc/trim": { - "content": [ - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", - "WT_REP1_trimmed_1_val_1_fastqc.html", - "WT_REP1_trimmed_1_val_1_fastqc.zip", - "WT_REP1_trimmed_2_val_2_fastqc.html", - "WT_REP1_trimmed_2_val_2_fastqc.zip", - "WT_REP2_trimmed_1_val_1_fastqc.html", - "WT_REP2_trimmed_1_val_1_fastqc.zip", - "WT_REP2_trimmed_2_val_2_fastqc.html", - "WT_REP2_trimmed_2_val_2_fastqc.zip" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T18:00:10.790876" - }, - "star_salmon/dupradar": { - "content": [ - "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,ddadea4a08511aae6faeb632eb6aafea", - "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,1db4c86723cf69052c4386760a9750bb", - "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,c0bf1135d2d70c5918d87f706c0c54bc", - "WT_REP1_dupMatrix.txt:md5,b0de1683f2a9bfa42437e924a11648fd", - "WT_REP2_dupMatrix.txt:md5,bab18079153627205e5d907d8dfba677", - "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,b21a53b0156b0afdfc28c237cb11218d", - "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,eccc5ca37855c717d35477e684188695", - "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,c3900f3bb24cd339d0e0ecf65ae43217", - "WT_REP1_intercept_slope.txt:md5,f38c8525b7fcb990b7158f1518e451ad", - "WT_REP2_intercept_slope.txt:md5,9bcbc18d0d331fe3c972538456ffd5b2", - "RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf", - "RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf", - "RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf", - "WT_REP1_duprateExpBoxplot.pdf", - "WT_REP2_duprateExpBoxplot.pdf", - "RAP1_IAA_30M_REP1_expressionHist.pdf", - "RAP1_UNINDUCED_REP1_expressionHist.pdf", - "RAP1_UNINDUCED_REP2_expressionHist.pdf", - "WT_REP1_expressionHist.pdf", - "WT_REP2_expressionHist.pdf", - "RAP1_IAA_30M_REP1_duprateExpDens.pdf", - "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", - "RAP1_UNINDUCED_REP2_duprateExpDens.pdf", - "WT_REP1_duprateExpDens.pdf", - "WT_REP2_duprateExpDens.pdf" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T18:00:12.064305" - }, - "bbsplit": { - "content": [ - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T18:00:10.74095" - }, - "star_salmon/qualimap": { - "content": [ - "Coverage Profile Along Genes (High).png:md5,1a837e43161d7133e9156c7b18123aa9", - "Coverage Profile Along Genes (Low).png:md5,46c5ba09af49602b956efd780f7a39e4", - "Coverage Profile Along Genes (Total).png:md5,b04cac9c2d15b1b9623d87d44caadff6", - "Transcript coverage histogram.png:md5,cbb250c6903bfe6ecab5fb4b2ca661e5", - "coverage_profile_along_genes_(high).txt:md5,5aee6c959137a8c9bfbd0ddaa79dddba", - "coverage_profile_along_genes_(low).txt:md5,d2742410803e0de7cc606ef118010ea8", - "coverage_profile_along_genes_(total).txt:md5,d2742410803e0de7cc606ef118010ea8", - "Coverage Profile Along Genes (High).png:md5,8c8b46f9bfb6cf952a95d85a6b917444", - "Coverage Profile Along Genes (Low).png:md5,5c56671f085c6db7fd86b41bb5b7e6d0", - "Coverage Profile Along Genes (Total).png:md5,b83fbaedfe4dcfdd7b3970d2ff27d517", - "Transcript coverage histogram.png:md5,488440d7b6d73bcd4567316712e281fe", - "coverage_profile_along_genes_(high).txt:md5,f5ac8f74fcad5d9ac72dbb6b65184bd0", - "coverage_profile_along_genes_(low).txt:md5,d66da6e3f49b0870184fc881a162e785", - "coverage_profile_along_genes_(total).txt:md5,d66da6e3f49b0870184fc881a162e785", - "Coverage Profile Along Genes (High).png:md5,015aa34b0d32f38bade831a3ef497984", - "Coverage Profile Along Genes (Low).png:md5,5798e0d977e0fee55ec4fc5192bfc0f4", - "Coverage Profile Along Genes (Total).png:md5,2bbec5e165075024cb1f74a042b1385a", - "Transcript coverage histogram.png:md5,bfd09f8b3282958a6a73b7924edac664", - "coverage_profile_along_genes_(high).txt:md5,634f447f91db940d2148af74cf36febd", - "coverage_profile_along_genes_(low).txt:md5,db2e0acbe9f07c68bcd7e08e036f02d3", - "coverage_profile_along_genes_(total).txt:md5,db2e0acbe9f07c68bcd7e08e036f02d3", - "Coverage Profile Along Genes (High).png:md5,d8a36870a6f262c41995b4b5bd26a149", - "Coverage Profile Along Genes (Low).png:md5,5570af90ee685a3c95117519aa6bdc46", - "Coverage Profile Along Genes (Total).png:md5,eb53e699213ce453cbea7f71f5204b08", - "Transcript coverage histogram.png:md5,f0bd8d82a8b7adec6e1f1ef85633eded", - "coverage_profile_along_genes_(high).txt:md5,a349232d75f6c0adab6afcd9f6cbbafb", - "coverage_profile_along_genes_(low).txt:md5,b2c696661e6c524b1641eb7267c70edc", - "coverage_profile_along_genes_(total).txt:md5,b2c696661e6c524b1641eb7267c70edc", - "Coverage Profile Along Genes (High).png:md5,3c1c603d63f3f7f9ba1ab6e7749b7771", - "Coverage Profile Along Genes (Low).png:md5,9f80251ed043cf900fa939cc254ccc81", - "Coverage Profile Along Genes (Total).png:md5,a420f287f986a8db317be712ac0a2237", - "Transcript coverage histogram.png:md5,c467c5eac12a95f8569198927434440d", - "coverage_profile_along_genes_(high).txt:md5,3f76529bd723d5320c86cc407fbb3294", - "coverage_profile_along_genes_(low).txt:md5,b9be191fdec82c78057e083d3adf20dd", - "coverage_profile_along_genes_(total).txt:md5,b9be191fdec82c78057e083d3adf20dd", - "Junction Analysis.png", - "Reads Genomic Origin.png", - "qualimapReport.html", - "rnaseq_qc_results.txt", - "Junction Analysis.png", - "Reads Genomic Origin.png", - "qualimapReport.html", - "rnaseq_qc_results.txt", - "Junction Analysis.png", - "Reads Genomic Origin.png", - "qualimapReport.html", - "rnaseq_qc_results.txt", - "Junction Analysis.png", - "Reads Genomic Origin.png", - "qualimapReport.html", - "rnaseq_qc_results.txt", - "Junction Analysis.png", - "Reads Genomic Origin.png", - "qualimapReport.html", - "rnaseq_qc_results.txt" + { + "BBMAP_BBSPLIT": { + "bbmap": 39.01 + }, + "CAT_FASTQ": { + "cat": 8.3 + }, + "CUSTOM_CATADDITIONALFASTA": { + "python": null + }, + "CUSTOM_GETCHROMSIZES": { + "getchromsizes": 1.2 + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GTF2BED": { + "perl": "5.26.2" + }, + "GTF_FILTER": { + "python": "3.9.5" + }, + "GUNZIP_ADDITIONAL_FASTA": { + "gunzip": 1.1 + }, + "GUNZIP_GTF": { + "gunzip": 1.1 + }, + "SORTMERNA_INDEX": { + "sortmerna": "4.3.6" + }, + "STAR_GENOMEGENERATE": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "TRIMGALORE": { + "trimgalore": "0.6.7", + "cutadapt": 3.4 + }, + "UNTAR_SALMON_INDEX": { + "untar": 1.34 + }, + "Workflow": { + "nf-core/rnaseq": "v3.16.0dev" + } + }, + [ + "RAP1_IAA_30M_REP1_raw.html", + "RAP1_IAA_30M_REP1_raw.zip", + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_raw.html", + "RAP1_UNINDUCED_REP1_raw.zip", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_raw.html", + "RAP1_UNINDUCED_REP2_raw.zip", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_raw.html", + "WT_REP1_raw.zip", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_raw.html", + "WT_REP2_raw.zip", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt", + "custom", + "fastqc", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", + "multiqc", + "multiqc_data", + "multiqc_plots", + "multiqc_report.html", + "nf_core_rnaseq_software_mqc_versions.yml", + "out", + "pipeline_info", + "raw", + "star_salmon", + "trim", + "trimgalore" + ], + [ + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T13:19:36.107982" + "timestamp": "2024-09-13T11:49:33.901393" } } \ No newline at end of file diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index 9105ed9fa..530ce5ed3 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -15,216 +15,16 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name - ).match("bbsplit") }, - { assert snapshot( - path("${params.outdir}/custom/out/genome_gfp.fasta"), - path("${params.outdir}/custom/out/genome_gfp.gtf") - ).match("references") }, - { assert snapshot( - // HTMLs and ZIPs are not stable - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name - ).match("fastqc/trim") }, - { assert snapshot( - path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc-status-check-heatmap.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_counts_plot.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/multiqc_citations.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/multiqc_cutadapt.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), - // These files are not stable - file("${params.outdir}/multiqc/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, - file("${params.outdir}/multiqc/multiqc_report_data/multiqc_data.json").name, - file("${params.outdir}/multiqc/multiqc_report_data/multiqc_general_stats.txt").name, - file("${params.outdir}/multiqc/multiqc_report_data/multiqc_salmon.txt").name, - file("${params.outdir}/multiqc/multiqc_report_data/multiqc_software_versions.txt").name, - file("${params.outdir}/multiqc/multiqc_report_data/multiqc_sources.txt").name, - file("${params.outdir}/multiqc/multiqc_report_data/salmon_plot.txt").name - ).match("multiqc_data") }, - { assert snapshot( - path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), - // PDFs, SVGs, some PNGs and HTML reports are not stable - file("${params.outdir}/multiqc/multiqc_report.html").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/general_stats_table.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/pdf/salmon_plot.pdf").name, - file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, - file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, - file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, - file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, - file("${params.outdir}/multiqc/multiqc_report_plots/png/general_stats_table.png").name, - file("${params.outdir}/multiqc/multiqc_report_plots/png/salmon_plot.png").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/general_stats_table.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/salmon_plot.svg").name - ).match("multiqc_plots") }, + { assert workflow.success}, { assert snapshot( - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), - // These files are not stable - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP1/quant.sf").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP2/quant.sf").name - ).match("salmon_quant") }, - { assert snapshot( - path("${params.outdir}/salmon/tx2gene.tsv"), - // These files are not stable - file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name - ).match("salmon") }, - { assert snapshot( - // These reports are not stable - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name - ).match("trimgalore") }, - { assert snapshot( - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") - ).match("versions") } + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file_complement.collect { it.getName() }, + snapshottable_files + ).match() } ) } } @@ -243,31 +43,15 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, + { assert workflow.success}, { assert snapshot( UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, - file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, - file("${params.outdir}/multiqc/multiqc_report.html").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + file_complement.collect { it.getName() }, + snapshottable_files ).match() } ) } diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 004c15ad4..ea459fcea 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -1,297 +1,428 @@ { - "multiqc_data": { + "Params: --pseudo_aligner salmon --skip_qc --skip_alignment": { "content": [ - "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", - "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", - "fastqc-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", - "fastqc_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", - 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"salmon.merged.gene_tpm.tsv", - "salmon.merged.transcript_counts.SummarizedExperiment.rds", - "salmon.merged.transcript_counts.tsv", - "salmon.merged.transcript_lengths.tsv", - "salmon.merged.transcript_tpm.tsv" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-26T10:25:09.804203" - }, - "multiqc_plots": { - "content": [ - "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", - "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", - "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", - "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890", - "fastqc_overrepresented_sequences_plot.png:md5,40e450251b80ec0efc9364434234ec7f", - "fastqc_per_sequence_gc_content_plot_Counts.png:md5,8a806cec2142f9911502e0a253d83d13", - "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,953929d50c8490029880e205e4db7959", - "fastqc_per_sequence_quality_scores_plot.png:md5,d2c29cae169f35744500c751b4a7366e", - "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", - "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", - "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", - "multiqc_report.html", - "cutadapt_filtered_reads_plot-cnt.pdf", - "cutadapt_filtered_reads_plot-pct.pdf", - "cutadapt_trimmed_sequences_plot_3_Counts.pdf", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "fastqc-status-check-heatmap.pdf", - "fastqc_overrepresented_sequences_plot.pdf", - "fastqc_per_base_n_content_plot.pdf", - "fastqc_per_base_sequence_quality_plot.pdf", - "fastqc_per_sequence_gc_content_plot_Counts.pdf", - "fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "fastqc_per_sequence_quality_scores_plot.pdf", - "fastqc_sequence_counts_plot-cnt.pdf", - "fastqc_sequence_counts_plot-pct.pdf", - "fastqc_sequence_duplication_levels_plot.pdf", - "fastqc_sequence_length_distribution_plot.pdf", - "fastqc_top_overrepresented_sequences_table.pdf", - "general_stats_table.pdf", - "salmon_plot.pdf", - "fastqc_per_base_n_content_plot.png", - "fastqc_per_base_sequence_quality_plot.png", - "fastqc_sequence_length_distribution_plot.png", - "fastqc_top_overrepresented_sequences_table.png", - "general_stats_table.png", - "salmon_plot.png", - "cutadapt_filtered_reads_plot-cnt.svg", - "cutadapt_filtered_reads_plot-pct.svg", - "cutadapt_trimmed_sequences_plot_3_Counts.svg", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "fastqc-status-check-heatmap.svg", - "fastqc_overrepresented_sequences_plot.svg", - "fastqc_per_base_n_content_plot.svg", - "fastqc_per_base_sequence_quality_plot.svg", - "fastqc_per_sequence_gc_content_plot_Counts.svg", - "fastqc_per_sequence_gc_content_plot_Percentages.svg", - "fastqc_per_sequence_quality_scores_plot.svg", - "fastqc_sequence_counts_plot-cnt.svg", - "fastqc_sequence_counts_plot-pct.svg", - "fastqc_sequence_duplication_levels_plot.svg", - "fastqc_sequence_length_distribution_plot.svg", - "fastqc_top_overrepresented_sequences_table.svg", - "general_stats_table.svg", - "salmon_plot.svg" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-26T10:25:09.724424" - }, - "bbsplit": { - "content": [ - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-26T10:25:09.665867" - }, - "salmon_quant": { - "content": [ - "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", - "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", - "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", - "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", - "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", - "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", - "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", - "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", - "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", - "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-26T10:25:09.758031" + "timestamp": "2024-09-13T11:52:59.260944" }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", - "RAP1_IAA_30M_REP1_raw.html", - "RAP1_IAA_30M_REP1_raw.zip", - "RAP1_UNINDUCED_REP1_raw.html", - "RAP1_UNINDUCED_REP1_raw.zip", - "RAP1_UNINDUCED_REP2_raw.html", - "RAP1_UNINDUCED_REP2_raw.zip", - "WT_REP1_raw.html", - "WT_REP1_raw.zip", - "WT_REP2_raw.html", - "WT_REP2_raw.zip", - "multiqc_report.html", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + { + "BBMAP_BBSPLIT": { + "bbmap": 39.01 + }, + "CAT_FASTQ": { + "cat": 8.3 + }, + "CUSTOM_CATADDITIONALFASTA": { + "python": null + }, + "CUSTOM_GETCHROMSIZES": { + "getchromsizes": 1.2 + }, + "GTF2BED": { + "perl": "5.26.2" + }, + "GTF_FILTER": { + "python": "3.9.5" + }, + "GUNZIP_ADDITIONAL_FASTA": { + "gunzip": 1.1 + }, + "GUNZIP_GTF": { + "gunzip": 1.1 + }, + "TRIMGALORE": { + "trimgalore": "0.6.7", + "cutadapt": 3.4 + }, + "UNTAR_SALMON_INDEX": { + "untar": 1.34 + }, + "Workflow": { + "nf-core/rnaseq": "v3.16.0dev" + } + }, + [ + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt", + "custom", + "fastqc", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", + "multiqc", + "multiqc_data", + "multiqc_plots", + "multiqc_report.html", + "nf_core_rnaseq_software_mqc_versions.yml", + "out", + "pipeline_info", + "trim", + "trimgalore" + ], + [ + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T10:25:58.654392" + "timestamp": "2024-09-13T11:53:47.849117" } } \ No newline at end of file diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index 8fd703462..fc372d235 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -13,472 +13,16 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name - ).match("bbsplit") }, - { assert snapshot( - path("${params.outdir}/custom/out/genome_gfp.fasta"), - path("${params.outdir}/custom/out/genome_gfp.gtf") - ).match("references") }, - { assert snapshot( - // HTMLs and ZIPs are not stable - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name - ).match("fastqc/trim") }, - { assert snapshot( - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), - // These files are not stable - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name - ).match("multiqc_data") }, - { assert snapshot( - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), - // PDFs, SVGs, some PNGs and HTML reports are not stable - file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name - ).match("multiqc_plots") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name - ).match("star_salmon/samtools_stats") }, - { assert snapshot( - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab"), - // These files are not stable - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf").name - ).match("star_salmon/stringtie") }, - { assert snapshot( - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name - ).match("star_salmon/markdup") }, - { assert snapshot( - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), - // These files are not stable - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP1/quant.sf").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP2/quant.sf").name - ).match("salmon_quant") }, + { assert workflow.success}, { assert snapshot( - path("${params.outdir}/salmon/tx2gene.tsv"), - // These files are not stable - file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name - ).match("salmon") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig").name - ).match("star_salmon/bigwig") }, - { assert snapshot( - path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"), - // Logs are not stable - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name - ).match("star_salmon/log") }, - { assert snapshot( - // Metrics are not stable - file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name - ).match("star_salmon/picard_metrics") }, - { assert snapshot( - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"), - path("${params.outdir}/star_salmon/tx2gene.tsv"), - // These files are not stable - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name, - file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name, - file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name - ).match("star_salmon/salmon_quant") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name - ).match("star_salmon/salmon") }, - { assert snapshot( - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") - ).match("versions") } + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file_complement.collect { it.getName() }, + snapshottable_files + ).match() } ) } } @@ -495,31 +39,15 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, + { assert workflow.success}, { assert snapshot( UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, - file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + file_complement.collect { it.getName() }, + snapshottable_files ).match() } ) } diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 7a1eaccf3..a721f8cc5 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -1,596 +1,812 @@ { - "star_salmon/log": { - "content": [ - "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", - 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"ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", + "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", + "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", + "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", + "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", + "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", + "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", + "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", + "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", + "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", + "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", + "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", + "fastqc-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", + "fastqc_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", + "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c", + "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", + "fastqc_top_overrepresented_sequences_table.txt:md5,cf612406874da4e582eaeaa956f7eb66", + "flenDist.txt:md5,5bdd51baaad54a5d910a90ca9cb5437f", + "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", + "flenDist.txt:md5,236a3e518282fecf9e815eb0dd22683b", + "flenDist.txt:md5,7cbd44fc12e7736a2f1f1e6deb3faa74", + "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", + "flenDist.txt:md5,425385dfa0e5e690ac1ccde48b93ecd0", + "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", + "flenDist.txt:md5,d60bba7dd4bf325bc9f4c4ec57819d03", + "flenDist.txt:md5,bcbf5f1f5358db90b8553fb186cf559d", + "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", + "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", + "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", + "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", + "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", + "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", + "meta_info.json:md5,fe0d73479c8aab74d0419ad488a73487", + "meta_info.json:md5,daa42f959b5416e410e1c9912fc76be9", + "meta_info.json:md5,ff4d73b85b1cee2e19cc0ad036818b11", + "meta_info.json:md5,ffd0ca80f23ad695b3ba169b50c3a93e", + "meta_info.json:md5,cac0375eedfcad7817df18e28bfa50ba", + "meta_info.json:md5,ee69de2f03f56c2e65db8e9ddbbba1c5", + "meta_info.json:md5,f1d661cb5aa332fb52938657ed7693fb", + "meta_info.json:md5,1685dbd949da167dce5024857551da82", + "meta_info.json:md5,d0da723a07af4adf5866e11ef0f0e0ed", + "meta_info.json:md5,5d9dfc7a5f06ad51bf77344d03f6ab2c", + "multiqc_citations.txt:md5,ef51c78faebdd32bad296ba14406b41e", + "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", + "multiqc_general_stats.txt:md5,969a8f0aef8268da66150d723614dddd", + "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", + "multiqc_salmon.txt:md5,ee8f766c9af9f0d59e0391b3f6d71426", + "multiqc_samtools_flagstat.txt:md5,6cd62fbbb46370e90ff5410703f2891f", + "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", + "multiqc_samtools_stats.txt:md5,ae13ad7897ec9421a019c20c42f0ea71", + "multiqc_star.txt:md5,ae82337a5f847c86e8ffe14e04dfeaee", + "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", + "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "salmon.merged.gene_counts.tsv:md5,c14cab7e15cfac73ec0602dc2c404551", + "salmon.merged.gene_counts.tsv:md5,3ed7b1d514a12b2f431f7c72ae23dbe2", + "salmon.merged.gene_counts_length_scaled.tsv:md5,a3a07da2e891c40946b5f1ef2f6a27cf", + "salmon.merged.gene_counts_length_scaled.tsv:md5,481e23d26ea61c92458c28e07f3a1729", + "salmon.merged.gene_counts_scaled.tsv:md5,cd1b35911fd7be645c25d35196f50d3a", + "salmon.merged.gene_counts_scaled.tsv:md5,2eb656e29a548c404bb156ef2a94206d", + "salmon.merged.gene_lengths.tsv:md5,b40feaa838ffc98302527a59f9449784", + "salmon.merged.gene_lengths.tsv:md5,1b2eabc542ecf32844a84cb6bc790188", + "salmon.merged.gene_tpm.tsv:md5,76efd7f38e43a63be56697d403e47b22", + "salmon.merged.gene_tpm.tsv:md5,39027568743c7700f3fdcbd301889b18", + "salmon.merged.transcript_counts.tsv:md5,ff0f5be09ca7a322672c0074ba35da17", + "salmon.merged.transcript_counts.tsv:md5,12b3582c8f1dbd390d17dfbb324e08f2", + "salmon.merged.transcript_lengths.tsv:md5,9851a32c4e3ea0788510772bf377839e", + "salmon.merged.transcript_lengths.tsv:md5,62042bda6561146111ebc6456e9e984b", + "salmon.merged.transcript_tpm.tsv:md5,0c326a20ed5dd089367d85284719dce3", + "salmon.merged.transcript_tpm.tsv:md5,5dcfd83512b20e14769ff4c50c58a22f", + "salmon_plot.txt:md5,c1ee15b5ae91e69a6bd6170d7db57734", + "samtools-flagstat-dp_Percentage_of_total.txt:md5,f871d2c9eeb56efc70923843fe772353", + "samtools-flagstat-dp_Read_counts.txt:md5,11679c9decb6aabc056a2c05e4a56dec", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "samtools-stats-dp.txt:md5,b803784736c9eaf7c28f882071144ad7", + "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", + "star_alignment_plot.txt:md5,a44811c928719507cee0f98da7492fd1", + "star_summary_table.txt:md5,32aab6812d43f3c850b739eda99990f1", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T12:11:58.071145" + "timestamp": "2024-09-13T12:00:26.616669" } } \ No newline at end of file diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index e5b3aa080..a00a104ed 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -13,818 +13,18 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name - ).match("bbsplit") }, - { assert snapshot( - path("${params.outdir}/custom/out/genome_gfp.fasta"), - path("${params.outdir}/custom/out/genome_gfp.gtf") - ).match("references") }, - { assert snapshot( - // HTMLs and ZIPs are not stable - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name - ).match("fastqc/raw") }, - { assert snapshot( - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), - // These files are not stable - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name - ).match("multiqc_data") }, - { assert snapshot( - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), - // PDFs, SVGs, some PNGs and HTML reports are not stable - file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_bam_stat.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name - ).match("multiqc_plots") }, - { assert snapshot( - path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"), - // These files are not stable - file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name - ).match("salmon/deseq2_qc") }, - { assert snapshot( - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), - // These files are not stable - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP1/quant.sf").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP2/quant.sf").name - ).match("salmon_quant") }, - { assert snapshot( - path("${params.outdir}/salmon/tx2gene.tsv"), - // These files are not stable - file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name - ).match("salmon") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig").name, - file("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig").name - ).match("star_salmon/bigwig") }, - { assert snapshot( - path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), - // These files are not stable - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name, - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt").name - ).match("star_salmon/deseq2_qc") }, - { assert snapshot( - path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP1_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP2_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"), - // PDFs are not stable - file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP1_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP2_expressionHist.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name - ).match("star_salmon/dupradar") }, + { assert workflow.success}, { assert snapshot( - path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt"), - // These files are unstable - file("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name, - file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name, - file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name, - file("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt.summary").name, - file("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt.summary").name - ).match("star_salmon/featurecounts") }, - { assert snapshot( - path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"), - // Logs are not stable - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name, - file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name, - file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name, - file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name - ).match("star_salmon/log") }, - { assert snapshot( - // Metrics are not stable - file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name - ).match("star_salmon/picard_metrics") }, - { assert snapshot( - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - // HTML reports and these files are not stable - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt").name - ).match("star_salmon/qualimap") }, - { assert snapshot( - path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), - // PDFs, R scripts and all these files are not stable - file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name, - file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name - ).match("star_salmon/rseqc") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name - ).match("star_salmon/salmon") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name, - file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name - ).match("star_salmon/samtools_stats") }, - { assert snapshot( - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab"), - // These files are not stable - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP1.transcripts.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.coverage.gtf").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt").name, - file("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf").name - ).match("star_salmon/stringtie") }, - { assert snapshot( - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name - ).match("star_salmon/markdup") }, - { assert snapshot( - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"), - path("${params.outdir}/star_salmon/tx2gene.tsv"), - // These files are not stable - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name, - file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name, - file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name, - file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name, - file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name - ).match("star_salmon/salmon_quant") }, - { assert snapshot( - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") - ).match("versions") } + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file_complement.collect { it.getName() }, + snapshottable_files + ).match() } ) } } - // STUB ARE CURRENTLY NOT POSSIBLE - } diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 0cced5ad5..cbb165718 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -1,943 +1,1357 @@ { - "star_salmon/log": { + "Params: --skip_trimming": { "content": [ - "RAP1_IAA_30M_REP1.SJ.out.tab:md5,20c790387ef68e041bc4ffdcd032a22f", - "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,ba2636236fa1d26aa72f7aff73bd41f8", - "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1c0458f66e4af56a56f4409c120434b3", - "WT_REP1.SJ.out.tab:md5,299a948b1aaf329152224ba573402a51", - "WT_REP2.SJ.out.tab:md5,073498a8fb5fb4da664c9129a6777c42", - "RAP1_IAA_30M_REP1.Log.final.out", - "RAP1_IAA_30M_REP1.Log.out", - "RAP1_IAA_30M_REP1.Log.progress.out", - "RAP1_UNINDUCED_REP1.Log.final.out", - "RAP1_UNINDUCED_REP1.Log.out", - "RAP1_UNINDUCED_REP1.Log.progress.out", - "RAP1_UNINDUCED_REP2.Log.final.out", - "RAP1_UNINDUCED_REP2.Log.out", - "RAP1_UNINDUCED_REP2.Log.progress.out", - "WT_REP1.Log.final.out", - "WT_REP1.Log.out", - "WT_REP1.Log.progress.out", - "WT_REP2.Log.final.out", - "WT_REP2.Log.out", - "WT_REP2.Log.progress.out" + { + "BBMAP_BBSPLIT": { + "bbmap": 39.01 + }, + "BEDTOOLS_GENOMECOV_FW": { + "bedtools": "2.31.1" + }, + "CAT_FASTQ": { + "cat": 8.3 + }, + "CUSTOM_CATADDITIONALFASTA": { + "python": "3.9.5" + }, + "CUSTOM_GETCHROMSIZES": { + "getchromsizes": 1.2 + }, + "CUSTOM_TX2GENE": { + "python": "3.9.5" + }, + "DESEQ2_QC_PSEUDO": { + "r-base": "4.0.3", + "bioconductor-deseq2": "1.28.0" + }, + "DESEQ2_QC_STAR_SALMON": { + "r-base": "4.0.3", + "bioconductor-deseq2": "1.28.0" + }, + "DUPRADAR": { + "bioconductor-dupradar": "1.32.0" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "FQ_SUBSAMPLE": { + "fq": "0.9.1 (2022-02-22)" + }, + "GTF2BED": { + "perl": "5.26.2" + }, + "GTF_FILTER": { + "python": "3.9.5" + }, + "GUNZIP_ADDITIONAL_FASTA": { + "gunzip": 1.1 + }, + "GUNZIP_GTF": { + "gunzip": 1.1 + }, + "MULTIQC_CUSTOM_BIOTYPE": { + "python": "3.9.5" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.1.1" + }, + "QUALIMAP_RNASEQ": { + "qualimap": 2.3 + }, + "RSEQC_BAMSTAT": { + "rseqc": "5.0.2" + }, + "RSEQC_INFEREXPERIMENT": { + "rseqc": "5.0.2" + }, + "RSEQC_INNERDISTANCE": { + "rseqc": "5.0.2" + }, + "RSEQC_JUNCTIONANNOTATION": { + "rseqc": "5.0.2" + }, + "RSEQC_JUNCTIONSATURATION": { + "rseqc": "5.0.2" + }, + "RSEQC_READDISTRIBUTION": { + "rseqc": "5.0.2" + }, + "RSEQC_READDUPLICATION": { + "rseqc": "5.0.2" + }, + "SALMON_QUANT": { + "salmon": "1.10.1" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": 1.2 + }, + "SAMTOOLS_IDXSTATS": { + "samtools": 1.2 + }, + "SAMTOOLS_INDEX": { + "samtools": 1.2 + }, + "SAMTOOLS_SORT": { + "samtools": 1.2 + }, + "SAMTOOLS_STATS": { + "samtools": 1.2 + }, + "SE_GENE": { + "bioconductor-summarizedexperiment": "1.32.0" + }, + "STAR_ALIGN": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "STAR_GENOMEGENERATE": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "STRINGTIE_STRINGTIE": { + "stringtie": "2.2.1" + }, + "SUBREAD_FEATURECOUNTS": { + "subread": "2.0.1" + }, + "TXIMETA_TXIMPORT": { + "bioconductor-tximeta": "1.20.1" + }, + "UCSC_BEDCLIP": { + "ucsc": 377 + }, + "UCSC_BEDGRAPHTOBIGWIG": { + "ucsc": 445 + }, + 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"e_data.ctab:md5,9225250f729f9688c50718ad82989f4c", - "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", - "i_data.ctab:md5,319f3eaf67c02b6198a4d746f8b11a44", - "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", - "e_data.ctab:md5,1c69593079c7bff8b3e36b9d9aa616f9", - "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", - "i_data.ctab:md5,db2e9c245b5db90551b83c799194113c", - "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", - "e_data.ctab:md5,9628d551f88776248ace242ba43978e3", - "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", - "i_data.ctab:md5,50d273bef261ddb395260dc74eff1a8b", - "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", - "e_data.ctab:md5,9c0bf54804f5624b567481de8f5a5ae4", - "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", - "i_data.ctab:md5,d92fcfde4016a15c3f54340e8637e554", - "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", - "e_data.ctab:md5,3bddb4b7381a62a0104b7004e5b71f20", - "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", - "i_data.ctab:md5,cd4c62717bb0a0db1a17e9c6d8788599", - "t_data.ctab", - "RAP1_IAA_30M_REP1.coverage.gtf", - "RAP1_IAA_30M_REP1.gene.abundance.txt", - "RAP1_IAA_30M_REP1.transcripts.gtf", - "t_data.ctab", - "RAP1_UNINDUCED_REP1.coverage.gtf", - "RAP1_UNINDUCED_REP1.gene.abundance.txt", - "RAP1_UNINDUCED_REP1.transcripts.gtf", - "t_data.ctab", - "RAP1_UNINDUCED_REP2.coverage.gtf", - "RAP1_UNINDUCED_REP2.gene.abundance.txt", - "RAP1_UNINDUCED_REP2.transcripts.gtf", - "t_data.ctab", - "WT_REP1.coverage.gtf", - "WT_REP1.gene.abundance.txt", - "WT_REP1.transcripts.gtf", - "t_data.ctab", - "WT_REP2.coverage.gtf", - "WT_REP2.gene.abundance.txt", - "WT_REP2.transcripts.gtf" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-26T15:27:30.738255" - }, - "versions": { - "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-26T15:27:31.618005" - }, - "star_salmon/dupradar": { - "content": [ - "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,fdeebc4f056cbb52fee53e82c2e0096f", - "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,aa94a148bdbebec4e82cd18a00316506", - "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,bf065e266566c3fb96dc9319a3ed12cf", - "WT_REP1_dupMatrix.txt:md5,04512c8be70c1898d0262935ed5ec5bd", - "WT_REP2_dupMatrix.txt:md5,5052efd01f5086d394499b9c4626deb1", - "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,7962ee6ba989f9af6465aaf1101ba13b", - "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,6c69ccc819c14847eef319b7fa8ccb4f", - "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,147b051de3f1e5c75821176851d13612", - "WT_REP1_intercept_slope.txt:md5,395cde13da1a90cf4378be2597c4f297", - "WT_REP2_intercept_slope.txt:md5,7ddae43baa3c4e499fbc319b95627c41", - "RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf", - "RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf", - "RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf", - "WT_REP1_duprateExpBoxplot.pdf", - "WT_REP2_duprateExpBoxplot.pdf", - "RAP1_IAA_30M_REP1_expressionHist.pdf", - "RAP1_UNINDUCED_REP1_expressionHist.pdf", - "RAP1_UNINDUCED_REP2_expressionHist.pdf", - "WT_REP1_expressionHist.pdf", - "WT_REP2_expressionHist.pdf", - "RAP1_IAA_30M_REP1_duprateExpDens.pdf", - "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", - "RAP1_UNINDUCED_REP2_duprateExpDens.pdf", - "WT_REP1_duprateExpDens.pdf", - "WT_REP2_duprateExpDens.pdf" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-26T15:27:29.283253" - }, - "bbsplit": { - "content": [ - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-26T14:44:49.441331" - }, - "salmon_quant": { - "content": [ - "ambig_info.tsv:md5,e099a9ec06de792219139248712f7f40", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", - "lib_format_counts.json:md5,406e1457f0f0506bd8e605a217477436", - "ambig_info.tsv:md5,0e0895adb376929bec8e0dd0677bf7d8", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", - "lib_format_counts.json:md5,afd2a0ddf0fd0ec4f99be898608a59db", - "ambig_info.tsv:md5,6ed1b46c69917d6af3f093f9503bb962", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", - "lib_format_counts.json:md5,f7b7048fd2ac63fd792e71b85e4ed6d1", - "ambig_info.tsv:md5,2f4c6a5953e41252a89851a9a7c36d9b", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", - "lib_format_counts.json:md5,03f0b70a4bb428fab96c29f04f895b6f", - "ambig_info.tsv:md5,5fff63493bf3c223707ac90b9bb3a8f3", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", - "lib_format_counts.json:md5,4bf135c93c37f90c493f761f2709a28b", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-26T15:27:28.672506" - }, - "star_salmon/qualimap": { - "content": [ - "Coverage Profile Along Genes (High).png:md5,3a6e83a9a2e0e983b1191a622bfc8ef1", - "Coverage Profile Along Genes (Low).png:md5,1f075e71d4c281be2ecad16cf13f52bc", - "Coverage Profile Along Genes (Total).png:md5,f32d6ff38cfe4d01c6cbc917cb6e21c1", - "Transcript coverage histogram.png:md5,4e4a8d520a3018a888e5840936e9f4e0", - "coverage_profile_along_genes_(high).txt:md5,59a01cd5d9bc7b6096490d7f3d6d6877", - "coverage_profile_along_genes_(low).txt:md5,8a5255e6f9f142bbd22c636296f41d72", - "coverage_profile_along_genes_(total).txt:md5,8a5255e6f9f142bbd22c636296f41d72", - "Coverage Profile Along Genes (High).png:md5,a0efd6fc7c7c803a3b51e7fc4600ed98", - "Coverage Profile Along Genes (Low).png:md5,212d68ca87f5bc4c60ed04a33df126af", - "Coverage Profile Along Genes (Total).png:md5,a72b6252a3ece3fb911da724274eabae", - "Transcript coverage histogram.png:md5,1daabf214a2d2c32748834188c8bea5d", - "coverage_profile_along_genes_(high).txt:md5,61683a2fcf35174fe72a648be63d45ac", - "coverage_profile_along_genes_(low).txt:md5,031046ef33de379e0463fddc0b924ecd", - "coverage_profile_along_genes_(total).txt:md5,031046ef33de379e0463fddc0b924ecd", - "Coverage Profile Along Genes (High).png:md5,75dbf9d2b8bde265fdda486c050d5ff5", - "Coverage Profile Along Genes (Low).png:md5,8e792e6037158381a50e3668c54b7254", - "Coverage Profile Along Genes (Total).png:md5,beaf835a8aaf95df20815032a5f92622", - "Transcript coverage histogram.png:md5,6428ffa766e3c59ca42a9fb5e011d866", - "coverage_profile_along_genes_(high).txt:md5,2745780cc56258bbe587f9b6db03e9e4", - "coverage_profile_along_genes_(low).txt:md5,85154785601b18118ae2e6a19d0a1c0a", - "coverage_profile_along_genes_(total).txt:md5,85154785601b18118ae2e6a19d0a1c0a", - "Coverage Profile Along Genes (High).png:md5,6491fbf74a1444b98fdfe495b8c26a7f", - "Coverage Profile Along Genes (Low).png:md5,ee6b911d01b1cfbcebb5864a1f6f5fda", - "Coverage Profile Along Genes (Total).png:md5,f286514f978d5bcb9508a908068ff6c7", - "Transcript coverage histogram.png:md5,e925b300e71d23188aa45907e0754536", - "coverage_profile_along_genes_(high).txt:md5,6afb5ffc9ddad52f69c518e32118ac61", - "coverage_profile_along_genes_(low).txt:md5,248345fdf0f8de2a8d7d329edd0a5c42", - "coverage_profile_along_genes_(total).txt:md5,248345fdf0f8de2a8d7d329edd0a5c42", - "Coverage Profile Along Genes (High).png:md5,f9f0caee3156d32588c12daab8895a0f", - "Coverage Profile Along Genes (Low).png:md5,35ac4785ed0ffb80aaeec1fb26825f4b", - "Coverage Profile Along Genes (Total).png:md5,781cc1b68e9f7afc30a84b7e45b06f85", - "Transcript coverage histogram.png:md5,a4a300dc782deea67f18e516e0c50b3b", - "coverage_profile_along_genes_(high).txt:md5,f7c11dace9fc4f446fc29e5db7b3ee24", - "coverage_profile_along_genes_(low).txt:md5,f53cfe3e30c560e3261818c2e6df3d5d", - "coverage_profile_along_genes_(total).txt:md5,f53cfe3e30c560e3261818c2e6df3d5d", - "Junction Analysis.png", - "Reads Genomic Origin.png", - "qualimapReport.html", - "rnaseq_qc_results.txt", - "Junction Analysis.png", - "Reads Genomic Origin.png", - "qualimapReport.html", - "rnaseq_qc_results.txt", - "Junction Analysis.png", - "Reads Genomic Origin.png", - "qualimapReport.html", - "rnaseq_qc_results.txt", - "Junction Analysis.png", - "Reads Genomic Origin.png", - "qualimapReport.html", - "rnaseq_qc_results.txt", - "Junction Analysis.png", - "Reads Genomic Origin.png", - "qualimapReport.html", - "rnaseq_qc_results.txt" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-26T15:27:29.998661" + "timestamp": "2024-09-13T12:08:36.646809" } } \ No newline at end of file diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 0f03bc6db..b6421cb93 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -13,864 +13,16 @@ nextflow_pipeline { } then { - assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, - file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name - ).match("bbsplit") }, - { assert snapshot( - path("${params.outdir}/custom/out/genome_gfp.fasta"), - path("${params.outdir}/custom/out/genome_gfp.gtf") - ).match("references") }, - { assert snapshot( - // HTMLs and ZIPs are not stable - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name - ).match("fastqc/raw") }, - { assert snapshot( - // HTMLs and ZIPs are not stable - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, - file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, - file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name - ).match("fastqc/trim") }, - { assert snapshot( - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc-status-check-heatmap-1.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc-status-check-heatmap.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_adapter_content_plot.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_sequence_counts_plot.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_citations.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_cutadapt.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/picard_histogram.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/picard_histogram_1.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/picard_histogram_2.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), - // These files are not stable - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/junction_saturation_known.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/junction_saturation_novel.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_data.json").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_general_stats.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_picard_dups.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/picard_deduplication.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rsem.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_samtools_flagstat.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_samtools_stats.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_software_versions.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_sources.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_1.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_2.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_3.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_4.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_pca-plot.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_genomic_origin.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rsem_assignment_plot.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rsem_multimapping_rates.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_bam_stat.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_inner_distance.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_saturation_all.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_read_distribution_plot.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_read_dups.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_read_dups_plot.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/salmon_plot.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-stats-dp.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools_alignment_plot.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/star_alignment_plot.txt").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/star_summary_table.txt").name - ).match("multiqc_data") }, - { assert snapshot( + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/dupradar-section-plot.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rsem_multimapping_rates.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_dups_plot.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), - // PDFs, SVGs, some PNGs and HTML reports are not stable - file("${params.outdir}/multiqc/star_rsem/multiqc_report.html").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/general_stats_table.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rsem_assignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rsem_assignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rsem_multimapping_rates.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/salmon_plot.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/star_rsem_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/star_rsem_deseq2_pca-plot.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/star_summary_table.pdf").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fail_strand_check_table.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/general_stats_table.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/picard_deduplication-cnt.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/picard_deduplication-pct.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rsem_assignment_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rsem_assignment_plot-pct.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_bam_stat.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/salmon_plot.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-stats-dp.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_alignment_plot-pct.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_rsem_deseq2_clustering-plot.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_rsem_deseq2_pca-plot.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_summary_table.png").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/dupradar-section-plot.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fail_strand_check_table.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/general_stats_table.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/picard_deduplication-pct.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rsem_assignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rsem_assignment_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rsem_multimapping_rates.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_bam_stat.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/salmon_plot.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-stats-dp.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/star_rsem_deseq2_clustering-plot.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/star_rsem_deseq2_pca-plot.svg").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/star_summary_table.svg").name - ).match("multiqc_plots") }, - { assert snapshot( - path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"), - // These files are not stable - file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name, - file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name - ).match("salmon/deseq2_qc") }, - { assert snapshot( - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), - path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), - path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), - path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), - // These files are not stable - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP1/quant.sf").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, - file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, - file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, - file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, - file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, - file("${params.outdir}/salmon/WT_REP2/quant.sf").name - ).match("salmon_quant") }, - { assert snapshot( - path("${params.outdir}/salmon/tx2gene.tsv"), - // These files are not stable - file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, - file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name - ).match("salmon") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_rsem/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name, - file("${params.outdir}/star_rsem/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name, - file("${params.outdir}/star_rsem/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name, - file("${params.outdir}/star_rsem/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name, - file("${params.outdir}/star_rsem/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name, - file("${params.outdir}/star_rsem/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name, - file("${params.outdir}/star_rsem/bigwig/WT_REP1.forward.bigWig").name, - file("${params.outdir}/star_rsem/bigwig/WT_REP1.reverse.bigWig").name, - file("${params.outdir}/star_rsem/bigwig/WT_REP2.forward.bigWig").name, - file("${params.outdir}/star_rsem/bigwig/WT_REP2.reverse.bigWig").name - ).match("star_rsem/bigwig") }, - { assert snapshot( - path("${params.outdir}/star_rsem/deseq2_qc/R_sessionInfo.log"), - // These files are not stable - file("${params.outdir}/star_rsem/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, - file("${params.outdir}/star_rsem/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, - file("${params.outdir}/star_rsem/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, - file("${params.outdir}/star_rsem/deseq2_qc/size_factors/WT_REP1.txt").name, - file("${params.outdir}/star_rsem/deseq2_qc/size_factors/WT_REP2.txt").name, - file("${params.outdir}/star_rsem/deseq2_qc/size_factors/deseq2.size_factors.RData").name, - file("${params.outdir}/star_rsem/deseq2_qc/deseq2.dds.RData").name, - file("${params.outdir}/star_rsem/deseq2_qc/deseq2.pca.vals.txt").name, - file("${params.outdir}/star_rsem/deseq2_qc/deseq2.plots.pdf").name, - file("${params.outdir}/star_rsem/deseq2_qc/deseq2.sample.dists.txt").name - ).match("star_rsem/deseq2_qc") }, - { assert snapshot( - path("${params.outdir}/star_rsem/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"), - path("${params.outdir}/star_rsem/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"), - path("${params.outdir}/star_rsem/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"), - path("${params.outdir}/star_rsem/dupradar/gene_data/WT_REP1_dupMatrix.txt"), - path("${params.outdir}/star_rsem/dupradar/gene_data/WT_REP2_dupMatrix.txt"), - path("${params.outdir}/star_rsem/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"), - path("${params.outdir}/star_rsem/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"), - path("${params.outdir}/star_rsem/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"), - path("${params.outdir}/star_rsem/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"), - path("${params.outdir}/star_rsem/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"), - // PDFs are not stable - file("${params.outdir}/star_rsem/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_rsem/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_rsem/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_rsem/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_rsem/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name, - file("${params.outdir}/star_rsem/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name, - file("${params.outdir}/star_rsem/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name, - file("${params.outdir}/star_rsem/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name, - file("${params.outdir}/star_rsem/dupradar/histogram/WT_REP1_expressionHist.pdf").name, - file("${params.outdir}/star_rsem/dupradar/histogram/WT_REP2_expressionHist.pdf").name, - file("${params.outdir}/star_rsem/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/star_rsem/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/star_rsem/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name, - file("${params.outdir}/star_rsem/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name, - file("${params.outdir}/star_rsem/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name - ).match("star_rsem/dupradar") }, - { assert snapshot( - path("${params.outdir}/star_rsem/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_rsem/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_rsem/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"), - path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"), - path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"), - path("${params.outdir}/star_rsem/featurecounts/WT_REP1.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_rsem/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_rsem/featurecounts/WT_REP1.featureCounts.txt"), - path("${params.outdir}/star_rsem/featurecounts/WT_REP2.biotype_counts_mqc.tsv"), - path("${params.outdir}/star_rsem/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"), - path("${params.outdir}/star_rsem/featurecounts/WT_REP2.featureCounts.txt"), - // These files are unstable - file("${params.outdir}/star_rsem/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name, - file("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name, - file("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name, - file("${params.outdir}/star_rsem/featurecounts/WT_REP1.featureCounts.txt.summary").name, - file("${params.outdir}/star_rsem/featurecounts/WT_REP2.featureCounts.txt.summary").name - ).match("star_rsem/featurecounts") }, - { assert snapshot( - // These files are unstable - file("${params.outdir}/star_rsem/log/RAP1_IAA_30M_REP1.log").name, - file("${params.outdir}/star_rsem/log/RAP1_UNINDUCED_REP1.log").name, - file("${params.outdir}/star_rsem/log/RAP1_UNINDUCED_REP2.log").name, - file("${params.outdir}/star_rsem/log/WT_REP1.log").name, - file("${params.outdir}/star_rsem/log/WT_REP2.log").name - ).match("star_rsem/log") }, - { assert snapshot( - // Metrics are not stable - file("${params.outdir}/star_rsem/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_rsem/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_rsem/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_rsem/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, - file("${params.outdir}/star_rsem/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name - ).match("star_rsem/picard_metrics") }, - { assert snapshot( - path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_rsem/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_rsem/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_rsem/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), - path("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), - path("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_rsem/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), - path("${params.outdir}/star_rsem/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), - path("${params.outdir}/star_rsem/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - // HTML reports and these files are not stable - file("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, - file("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, - file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, - file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_rsem/qualimap/WT_REP1/qualimapReport.html").name, - file("${params.outdir}/star_rsem/qualimap/WT_REP1/rnaseq_qc_results.txt").name, - file("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name, - file("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name, - file("${params.outdir}/star_rsem/qualimap/WT_REP2/qualimapReport.html").name, - file("${params.outdir}/star_rsem/qualimap/WT_REP2/rnaseq_qc_results.txt").name - ).match("star_rsem/qualimap") }, - { assert snapshot( - path("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.genes.results"), - path("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.isoforms.results"), - path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.genes.results"), - path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.isoforms.results"), - path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.genes.results"), - path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.isoforms.results"), - path("${params.outdir}/star_rsem/WT_REP1.genes.results"), - path("${params.outdir}/star_rsem/WT_REP1.isoforms.results"), - path("${params.outdir}/star_rsem/WT_REP2.genes.results"), - path("${params.outdir}/star_rsem/WT_REP2.isoforms.results"), - path("${params.outdir}/star_rsem/rsem.merged.gene_counts.tsv"), - path("${params.outdir}/star_rsem/rsem.merged.gene_tpm.tsv"), - path("${params.outdir}/star_rsem/rsem.merged.transcript_counts.tsv"), - path("${params.outdir}/star_rsem/rsem.merged.transcript_tpm.tsv"), - // These files are not stable - file("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.stat/RAP1_IAA_30M_REP1.cnt").name, - file("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.stat/RAP1_IAA_30M_REP1.model").name, - file("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.stat/RAP1_IAA_30M_REP1.theta").name, - file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.stat/RAP1_UNINDUCED_REP1.cnt").name, - file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.stat/RAP1_UNINDUCED_REP1.model").name, - file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.stat/RAP1_UNINDUCED_REP1.theta").name, - file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.stat/RAP1_UNINDUCED_REP2.cnt").name, - file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.stat/RAP1_UNINDUCED_REP2.model").name, - file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.stat/RAP1_UNINDUCED_REP2.theta").name, - file("${params.outdir}/star_rsem/WT_REP1.stat/WT_REP1.cnt").name, - file("${params.outdir}/star_rsem/WT_REP1.stat/WT_REP1.model").name, - file("${params.outdir}/star_rsem/WT_REP1.stat/WT_REP1.theta").name, - file("${params.outdir}/star_rsem/WT_REP2.stat/WT_REP2.cnt").name, - file("${params.outdir}/star_rsem/WT_REP2.stat/WT_REP2.model").name, - file("${params.outdir}/star_rsem/WT_REP2.stat/WT_REP2.theta").name - ).match("star_rsem/rsem") }, - { assert snapshot( - path("${params.outdir}/star_rsem/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), - path("${params.outdir}/star_rsem/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), - path("${params.outdir}/star_rsem/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), - path("${params.outdir}/star_rsem/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), - path("${params.outdir}/star_rsem/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), - // PDFs, R scripts and all these files are not stable - file("${params.outdir}/star_rsem/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name, - file("${params.outdir}/star_rsem/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name, - file("${params.outdir}/star_rsem/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name, - file("${params.outdir}/star_rsem/rseqc/bam_stat/WT_REP1.bam_stat.txt").name, - file("${params.outdir}/star_rsem/rseqc/bam_stat/WT_REP2.bam_stat.txt").name, - file("${params.outdir}/star_rsem/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, - file("${params.outdir}/star_rsem/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name, - file("${params.outdir}/star_rsem/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name, - file("${params.outdir}/star_rsem/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name, - file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name, - file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name, - file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name, - file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name, - file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name, - file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name, - file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name, - file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name, - file("${params.outdir}/star_rsem/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name, - file("${params.outdir}/star_rsem/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_rsem/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_rsem/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_rsem/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_rsem/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name, - file("${params.outdir}/star_rsem/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name, - file("${params.outdir}/star_rsem/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name, - file("${params.outdir}/star_rsem/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name, - file("${params.outdir}/star_rsem/rseqc/read_distribution/WT_REP1.read_distribution.txt").name, - file("${params.outdir}/star_rsem/rseqc/read_distribution/WT_REP2.read_distribution.txt").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name, - file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name - ).match("star_rsem/rseqc") }, - { assert snapshot( - // These files are not stable - file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name, - file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name, - file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, - file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.sorted.bam.flagstat").name, - file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.sorted.bam.idxstats").name, - file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.sorted.bam.stats").name, - file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name, - file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name, - file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, - file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.sorted.bam.flagstat").name, - file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.sorted.bam.idxstats").name, - file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.sorted.bam.stats").name - ).match("star_rsem/samtools_stats") }, - { assert snapshot( - path("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"), - path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"), - path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"), - path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"), - path("${params.outdir}/star_rsem/stringtie/WT_REP1.ballgown/e2t.ctab"), - path("${params.outdir}/star_rsem/stringtie/WT_REP1.ballgown/e_data.ctab"), - path("${params.outdir}/star_rsem/stringtie/WT_REP1.ballgown/i2t.ctab"), - path("${params.outdir}/star_rsem/stringtie/WT_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_rsem/stringtie/WT_REP2.ballgown/e2t.ctab"), - path("${params.outdir}/star_rsem/stringtie/WT_REP2.ballgown/e_data.ctab"), - path("${params.outdir}/star_rsem/stringtie/WT_REP2.ballgown/i2t.ctab"), - path("${params.outdir}/star_rsem/stringtie/WT_REP2.ballgown/i_data.ctab"), - // These files are not stable - file("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name, - file("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name, - file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name, - file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name, - file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name, - file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name, - file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name, - file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name, - file("${params.outdir}/star_rsem/stringtie/WT_REP1.ballgown/t_data.ctab").name, - file("${params.outdir}/star_rsem/stringtie/WT_REP1.coverage.gtf").name, - file("${params.outdir}/star_rsem/stringtie/WT_REP1.gene.abundance.txt").name, - file("${params.outdir}/star_rsem/stringtie/WT_REP1.transcripts.gtf").name, - file("${params.outdir}/star_rsem/stringtie/WT_REP2.ballgown/t_data.ctab").name, - file("${params.outdir}/star_rsem/stringtie/WT_REP2.coverage.gtf").name, - file("${params.outdir}/star_rsem/stringtie/WT_REP2.gene.abundance.txt").name, - file("${params.outdir}/star_rsem/stringtie/WT_REP2.transcripts.gtf").name - ).match("star_rsem/stringtie") }, - { assert snapshot( - file("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, - file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_rsem/WT_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_rsem/WT_REP1.markdup.sorted.bam.bai").name, - file("${params.outdir}/star_rsem/WT_REP2.markdup.sorted.bam").name, - file("${params.outdir}/star_rsem/WT_REP2.markdup.sorted.bam.bai").name - ).match("star_rsem/markdup") }, - { assert snapshot( - // These reports are not stable - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name - ).match("trimgalore") }, + assertAll( + { assert workflow.success}, { assert snapshot( - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") - ).match("versions") } + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file_complement.collect { it.getName() }, + snapshottable_files + ).match() } ) } } @@ -887,31 +39,15 @@ nextflow_pipeline { } then { + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + assertAll( - { assert workflow.success }, + { assert workflow.success}, { assert snapshot( UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, - file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, - file("${params.outdir}/multiqc/star_rsem/multiqc_report.html").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, - file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + file_complement.collect { it.getName() }, + snapshottable_files ).match() } ) } diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index a6a804341..aeb02255c 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -1,1029 +1,1477 @@ { - "star_rsem/bigwig": { + "Params: --aligner star_rsem": { "content": [ - "RAP1_IAA_30M_REP1.forward.bigWig", - "RAP1_IAA_30M_REP1.reverse.bigWig", - "RAP1_UNINDUCED_REP1.forward.bigWig", - "RAP1_UNINDUCED_REP1.reverse.bigWig", - "RAP1_UNINDUCED_REP2.forward.bigWig", - "RAP1_UNINDUCED_REP2.reverse.bigWig", - "WT_REP1.forward.bigWig", - "WT_REP1.reverse.bigWig", - "WT_REP2.forward.bigWig", - "WT_REP2.reverse.bigWig" + { + "BBMAP_BBSPLIT": { + "bbmap": 39.01 + }, + "BEDTOOLS_GENOMECOV_FW": { + "bedtools": "2.31.1" + }, + "CAT_FASTQ": { + "cat": 8.3 + }, + "CUSTOM_CATADDITIONALFASTA": { + "python": "3.9.5" + }, + "CUSTOM_GETCHROMSIZES": { + "getchromsizes": 1.2 + }, + "CUSTOM_TX2GENE": { + "python": "3.9.5" + }, + "DESEQ2_QC_PSEUDO": { + "r-base": "4.0.3", + "bioconductor-deseq2": "1.28.0" + }, + "DESEQ2_QC_RSEM": { + "r-base": "4.0.3", + "bioconductor-deseq2": "1.28.0" + }, + "DUPRADAR": { + "bioconductor-dupradar": "1.32.0" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "FQ_SUBSAMPLE": { + "fq": "0.9.1 (2022-02-22)" + }, + "GTF2BED": { + "perl": "5.26.2" + }, + "GTF_FILTER": { + "python": "3.9.5" + }, + "GUNZIP_ADDITIONAL_FASTA": { + "gunzip": 1.1 + }, + "GUNZIP_GTF": { + "gunzip": 1.1 + }, + "MULTIQC_CUSTOM_BIOTYPE": { + "python": "3.9.5" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.1.1" + }, + "QUALIMAP_RNASEQ": { + "qualimap": 2.3 + }, + "RSEM_CALCULATEEXPRESSION": { + "rsem": "1.3.1", + "star": "2.7.10a" + }, + "RSEM_MERGE_COUNTS": { + "sed": 4.7 + }, + "RSEQC_BAMSTAT": { + "rseqc": "5.0.2" + }, + "RSEQC_INFEREXPERIMENT": { + "rseqc": "5.0.2" + }, + "RSEQC_INNERDISTANCE": { + "rseqc": "5.0.2" + }, + "RSEQC_JUNCTIONANNOTATION": { + "rseqc": "5.0.2" + }, + "RSEQC_JUNCTIONSATURATION": { + "rseqc": "5.0.2" + }, + "RSEQC_READDISTRIBUTION": { + "rseqc": "5.0.2" + }, + "RSEQC_READDUPLICATION": { + "rseqc": "5.0.2" + }, + "SALMON_QUANT": { + "salmon": "1.10.1" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": 1.2 + }, + "SAMTOOLS_IDXSTATS": { + "samtools": 1.2 + }, + "SAMTOOLS_INDEX": { + "samtools": 1.2 + }, + "SAMTOOLS_SORT": { + "samtools": 1.2 + }, + "SAMTOOLS_STATS": { + "samtools": 1.2 + }, + "SE_GENE": { + "bioconductor-summarizedexperiment": "1.32.0" + }, + "STRINGTIE_STRINGTIE": { + "stringtie": "2.2.1" + }, + "SUBREAD_FEATURECOUNTS": { + "subread": "2.0.1" + }, + "TRIMGALORE": { + "trimgalore": "0.6.7", + "cutadapt": 3.4 + }, + "TXIMETA_TXIMPORT": { + "bioconductor-tximeta": "1.20.1" + }, + "UCSC_BEDCLIP": { + "ucsc": 377 + }, + "UCSC_BEDGRAPHTOBIGWIG": { + "ucsc": 445 + }, + "UNTAR_RSEM_INDEX": { + "untar": 1.34 + }, + "UNTAR_SALMON_INDEX": { + "untar": 1.34 + }, + "Workflow": { + "nf-core/rnaseq": "v3.16.0dev" + } + }, + [ + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", + "Coverage Profile Along Genes (Total).png", + "Coverage Profile Along Genes (Total).png", + "Coverage Profile Along Genes (Total).png", + "Coverage Profile Along Genes (Total).png", + "Junction Analysis.png", + "Junction Analysis.png", + "Junction Analysis.png", + "Junction Analysis.png", + "Junction Analysis.png", + "RAP1_IAA_30M_REP1", + "RAP1_IAA_30M_REP1", + "RAP1_IAA_30M_REP1.DupRate_plot.pdf", + "RAP1_IAA_30M_REP1.DupRate_plot.r", + "RAP1_IAA_30M_REP1.ballgown", + "RAP1_IAA_30M_REP1.bam_stat.txt", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv", + "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv", + "RAP1_IAA_30M_REP1.cnt", + "RAP1_IAA_30M_REP1.coverage.gtf", + "RAP1_IAA_30M_REP1.featureCounts.txt", + "RAP1_IAA_30M_REP1.featureCounts.txt.summary", + "RAP1_IAA_30M_REP1.forward.bigWig", + "RAP1_IAA_30M_REP1.gene.abundance.txt", + "RAP1_IAA_30M_REP1.genes.results", + "RAP1_IAA_30M_REP1.infer_experiment.txt", + "RAP1_IAA_30M_REP1.inner_distance.txt", + "RAP1_IAA_30M_REP1.inner_distance_freq.txt", + "RAP1_IAA_30M_REP1.inner_distance_mean.txt", + "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", + "RAP1_IAA_30M_REP1.inner_distance_plot.r", + "RAP1_IAA_30M_REP1.isoforms.results", + "RAP1_IAA_30M_REP1.junction.Interact.bed", + "RAP1_IAA_30M_REP1.junction.bed", + "RAP1_IAA_30M_REP1.junction.xls", + "RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf", + "RAP1_IAA_30M_REP1.junctionSaturation_plot.r", + "RAP1_IAA_30M_REP1.junction_annotation.log", + "RAP1_IAA_30M_REP1.junction_plot.r", + "RAP1_IAA_30M_REP1.log", + "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", + "RAP1_IAA_30M_REP1.markdup.sorted.bam", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.model", + "RAP1_IAA_30M_REP1.pos.DupRate.xls", + "RAP1_IAA_30M_REP1.read_distribution.txt", + "RAP1_IAA_30M_REP1.reverse.bigWig", + "RAP1_IAA_30M_REP1.seq.DupRate.xls", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", + "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_IAA_30M_REP1.splice_events.pdf", + "RAP1_IAA_30M_REP1.splice_junction.pdf", + "RAP1_IAA_30M_REP1.stat", + "RAP1_IAA_30M_REP1.stats.txt", + "RAP1_IAA_30M_REP1.theta", + "RAP1_IAA_30M_REP1.transcripts.gtf", + "RAP1_IAA_30M_REP1.txt", + "RAP1_IAA_30M_REP1.txt", + "RAP1_IAA_30M_REP1_dupMatrix.txt", + "RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf", + "RAP1_IAA_30M_REP1_duprateExpDens.pdf", + "RAP1_IAA_30M_REP1_expressionHist.pdf", + "RAP1_IAA_30M_REP1_intercept_slope.txt", + "RAP1_IAA_30M_REP1_raw_1_fastqc.html", + "RAP1_IAA_30M_REP1_raw_1_fastqc.zip", + 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d145a1b8c4324cd2e25206d00f79c8429578313c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Sep 2024 18:07:29 +0200 Subject: [PATCH 038/100] update half of all snaps --- tests/default.nf.test.snap | 161 +-------- tests/featurecounts_group_type.nf.test.snap | 161 +-------- tests/hisat2.nf.test.snap | 131 +------ tests/kallisto.nf.test.snap | 60 ++-- tests/lib/UTILS.groovy | 359 +++++++++++++++++++- 5 files changed, 374 insertions(+), 498 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 2b4e1e8bc..1c445c8ca 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -81,21 +81,14 @@ "trimgalore" ], [ - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - 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"flenDist.txt:md5,fcd14ae0bb313eef69c4b68679388e18", - "flenDist.txt:md5,c48c5f6934cdeea834b65a20503f12ad", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "junction_saturation_known.txt:md5,a9a4fdd482d8dc86a22923d761298853", - "junction_saturation_novel.txt:md5,07b5d9d7ae29353157b0d4de5412f7f9", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", - "meta_info.json:md5,28af84da71894574f44941a1f1e299c4", - "meta_info.json:md5,f4541837f355dae5ee394af161fad0fc", - "meta_info.json:md5,c952934e97ecc7cf97b809ba178047a6", - "meta_info.json:md5,0a479926725a69f05e5a255eda8da05a", - "meta_info.json:md5,8574e4f73d8f6bfc57655b0532dd63ed", - "meta_info.json:md5,ea43e53c34fffe464b28f10f20b9f022", - "meta_info.json:md5,df43f43d123f5d4971765385223f07a7", - "meta_info.json:md5,2de3741bf75b839d357b69ca2d851a92", - "meta_info.json:md5,37b69a9bc5c9efc101e72cccc33c7714", - "meta_info.json:md5,bd547581ecb886452b6f845d724c0c03", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_dupradar-section-plot.txt:md5,670aad5e7349a77c6b1e3d46ed03c2f7", - "multiqc_fail_strand_check_table.txt:md5,dbfc10fcab08e287a7c2bae40d26e3d7", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,56be7f0813c3cbea0f68f61d9b355b71", - "multiqc_general_stats.txt:md5,1646098b9a057635ef1fcfeb33189b53", - "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", - "multiqc_rseqc_bam_stat.txt:md5,1aa9eeb5b9d283ba77e98f0f5ea0f712", - "multiqc_rseqc_infer_experiment.txt:md5,475b85d8065528e9674a74d2d43644ab", - "multiqc_rseqc_junction_annotation.txt:md5,e78e23f7f32cc2c58136df6ed89d7638", - "multiqc_rseqc_read_distribution.txt:md5,b7106d48346fe4150a8094ef1744f8b3", - "multiqc_salmon.txt:md5,c7368ba3d628d55d14a48a1664d0deca", - "multiqc_salmon_deseq2_clustering-plot.txt:md5,c39fd219828df33259e48aadcdd1997c", - "multiqc_salmon_deseq2_clustering-plot_1.txt:md5,6ccabfcdd11d36e140a7d6615c73ae85", - "multiqc_salmon_deseq2_clustering-plot_2.txt:md5,792ce8a58aefbbd10c0f182fcbc37c7a", - "multiqc_salmon_deseq2_clustering-plot_3.txt:md5,3080d13dee6e437084f27937296ede8a", - "multiqc_salmon_deseq2_clustering-plot_4.txt:md5,c750d2fa8d6dc8a2370335a71d2fa637", - "multiqc_salmon_deseq2_pca-plot.txt:md5,831426c001fe69be0e1ab2bfe32a234b", - "multiqc_samtools_flagstat.txt:md5,58b88d6bd59c226507d971fd9638405b", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "multiqc_samtools_stats.txt:md5,ad855d27b46822dbb701621fad3cc43f", - "multiqc_star.txt:md5,b3dc9dd2d290f12b8835758654a29edd", - "multiqc_star_salmon_deseq2_clustering-plot.txt:md5,72d5b6d429709160351d875524a50a7c", - "multiqc_star_salmon_deseq2_clustering-plot_1.txt:md5,37a19cbfb14a04455b57b6160d4ef25e", - "multiqc_star_salmon_deseq2_clustering-plot_2.txt:md5,ebad3b29617432485579000fb421958b", - "multiqc_star_salmon_deseq2_clustering-plot_3.txt:md5,0623170a882f18ef18387da6df69a650", - "multiqc_star_salmon_deseq2_clustering-plot_4.txt:md5,ebaa497884793b38eef593d98516ecc9", - "multiqc_star_salmon_deseq2_pca-plot.txt:md5,be897cdf8bba2b37249925f42a3dceae", - "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,02044ed1bf1eca19a8a87c9971cdc049", "qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa", - "qualimap_genomic_origin.txt:md5,bf9f1cba02195a298fb54c984c3269a6", "qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce", - "qualimap_rnaseq_genome_results.txt:md5,ce5f4f7f5afa8f1e5666f738c4f414e7", - "rnaseq_qc_results.txt:md5,6bb8c2b18eb67b015bba7d92944cd687", - "rnaseq_qc_results.txt:md5,3eed764ef657161586b04670aad512d6", - "rnaseq_qc_results.txt:md5,401d4141bd4d884b35faa4cb497311f7", - "rnaseq_qc_results.txt:md5,fdf42ac95316d03a8ed66ab87d1b3d23", - "rnaseq_qc_results.txt:md5,9c6543bf977cea9624aab0d2c0eb2640", - "rseqc_bam_stat.txt:md5,ba2575875efaf137f8bf7c2b790d5b1b", "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", - "rseqc_inner_distance.txt:md5,33a445ddf5841156362e908d62ab2a81", - "rseqc_inner_distance_plot_Counts.txt:md5,04561343fab91ad7e1e285f5816cf740", - "rseqc_inner_distance_plot_Percentages.txt:md5,92f40f2969a02e28a70b94ae78be045a", - "rseqc_junction_annotation_junctions_plot_Events.txt:md5,90f1fabea84aa36f647b980978d01e58", - "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,454eb9917793890ee4837fce43e3a8dd", - "rseqc_junction_saturation_all.txt:md5,144763c0da8891088ac98cf9b316cb5b", - "rseqc_junction_saturation_plot_All_Junctions.txt:md5,91ab7eac92f93e516ffc01a87977eba4", - "rseqc_junction_saturation_plot_Known_Junctions.txt:md5,0a405852c4b74c2031b782792baf4185", - "rseqc_junction_saturation_plot_Novel_Junctions.txt:md5,1daf2f820278df5a983be82bb0908271", - "rseqc_read_distribution_plot.txt:md5,48cea394a38d0f0ed3044b0a54638e65", - "rseqc_read_dups.txt:md5,e2df2dfd0a1acf5466c4b430330e15cd", - "rseqc_read_dups_plot.txt:md5,a9f437a3a7eaeb2709fa63644de16ea0", - "salmon.merged.gene_counts.tsv:md5,c14cab7e15cfac73ec0602dc2c404551", - "salmon.merged.gene_counts.tsv:md5,409576c08b219c6042cd9ee6865e6eac", - "salmon.merged.gene_counts_length_scaled.tsv:md5,a5ab2399bad77aea792b573d9aa2d2a9", - "salmon.merged.gene_counts_length_scaled.tsv:md5,880121f4cd7018d570df5a358c537df7", - "salmon.merged.gene_counts_scaled.tsv:md5,03c19bcf24070b5d2fc34d9dba1cd5f1", - "salmon.merged.gene_counts_scaled.tsv:md5,16d3e8dbeeb9710ebc208f8500b8687e", - "salmon.merged.gene_lengths.tsv:md5,de21d96e853159c7a2aff17cb1561800", - "salmon.merged.gene_lengths.tsv:md5,51e6035807aaaf5cdef3be3b906a65d9", - "salmon.merged.gene_tpm.tsv:md5,750651ebf5c4eb9e6ee9d49884ae6ab1", - "salmon.merged.gene_tpm.tsv:md5,5de927eec799249ef500f854a8096a2a", - "salmon.merged.transcript_counts.tsv:md5,ff0f5be09ca7a322672c0074ba35da17", - "salmon.merged.transcript_counts.tsv:md5,f5a3b4ee4edf754809792170f6a298e3", - "salmon.merged.transcript_lengths.tsv:md5,365c48741fe7b4978cd9a41c06523a21", - "salmon.merged.transcript_lengths.tsv:md5,0573be60d15c96f8aff8e01de650d5a3", - "salmon.merged.transcript_tpm.tsv:md5,6cf7047adabdd6084f4e273f54627214", - "salmon.merged.transcript_tpm.tsv:md5,ac804d1e2c4c344637449b1b62119a14", - "salmon_plot.txt:md5,5ec8f191683341725ad78425052bdc24", - "samtools-flagstat-dp_Percentage_of_total.txt:md5,4539f2d516dd8041a89468b71f1bc44f", - "samtools-flagstat-dp_Read_counts.txt:md5,382a459fe7651ed28fdf2923873a4564", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", - "samtools-stats-dp.txt:md5,3ad92aaf2ee90b0813e44a63ed695551", - "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", - "star_alignment_plot.txt:md5,77fc30308bc1b75bcf6e99630fc15344", - "star_summary_table.txt:md5,188cd28a8f309eb7c095694d79920eda", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] @@ -1568,6 +1413,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T11:08:19.790408" + "timestamp": "2024-09-13T17:41:17.28886" } } \ No newline at end of file diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 925bd0df5..ff0d10d42 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -81,21 +81,14 @@ "trimgalore" ], [ - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T11:17:59.830188" + "timestamp": "2024-09-13T17:49:45.967217" }, "Params: --featurecounts_group_type false": { "content": [ @@ -1269,73 +1262,21 @@ "xls" ], [ - "RAP1_IAA_30M_REP1.bam_stat.txt:md5,b882e444c89be4ceed80e29865166b1a", - "RAP1_IAA_30M_REP1.gene.abundance.txt:md5,f9d863eb7c592dae0a150bb75e6dfb11", "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,169d25b95c008bebe9ce886fea6a4e33", - "RAP1_IAA_30M_REP1.inner_distance.txt:md5,0dfb9383c197b5e1db631a5000fd8fcf", - "RAP1_IAA_30M_REP1.inner_distance_freq.txt:md5,0d3b00e36f5afa9c058fb3a99a5d9dcf", - "RAP1_IAA_30M_REP1.inner_distance_mean.txt:md5,002a82a3fb9fe6eb58e2dce854a5922f", - 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"WT_REP2.inner_distance_mean.txt:md5,74177bfbb70daf8bdc3557b3253089b8", - "WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt:md5,3b45bc18911272011613ad4a92e74b1f", - "WT_REP2.read_distribution.txt:md5,c11d02cba5674017b90c8372abee3e39", - "WT_REP2.stats.txt:md5,002ddf6b828d34979652a40f05462843", - "WT_REP2.txt:md5,3761cdcd554d5b696a42fd83f0f4cab7", - "WT_REP2.txt:md5,c23242f9bc76f5528d17d869554c8d2c", "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5", "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,5cc2f7906296766ab64ed74f58a6cc7e", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,a8bed8dda99e21e266e590c0c1c1c863", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", @@ -1374,10 +1315,6 @@ "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", - "deseq2.pca.vals.txt:md5,1c67cac64dbcad0e8d83d84b5636c3e2", - "deseq2.pca.vals.txt:md5,159d70e157d4273cbf7121a06208a536", - "deseq2.sample.dists.txt:md5,5e9881e1e97a13230435e116dee981f9", - "deseq2.sample.dists.txt:md5,c27be3cc1cb2f5c6f663dfe7d538eff3", "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", @@ -1398,118 +1335,26 @@ "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "fastqc_top_overrepresented_sequences_table-1.txt:md5,fbd6b1f651b8fbe108b05a19e9ba7ca7", - "fastqc_top_overrepresented_sequences_table.txt:md5,a415f85e91e40b3e33495c8966b589e6", - "flenDist.txt:md5,43ef9812ccd1c61c41fd03fe20b29e3e", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "flenDist.txt:md5,7de4516be3cc8d9339c9e245286ebaec", - "flenDist.txt:md5,944b7e9b011aa659848596d33a22991b", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "flenDist.txt:md5,83603c5784a7cddc304a7d0a53660c94", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "flenDist.txt:md5,b7808dd650470f30730f55819fe070fd", - "flenDist.txt:md5,0a0798ae1b15e73ccb2fe671dd0db1f5", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "junction_saturation_known.txt:md5,fc168116148ddc010e3247499e35b3a7", - "junction_saturation_novel.txt:md5,57499d7895d2af954961b7af98e26266", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", - "meta_info.json:md5,b539b9fa0b7a5698ecda991d8f92a860", - "meta_info.json:md5,d8608fb6439e5e0632acfc9d5681c755", - "meta_info.json:md5,13d7f9f021532a3f5b4ca3b1e04b1deb", - "meta_info.json:md5,49566d41ad3ed6db89e523a701bcef6e", - "meta_info.json:md5,92e033fdb0f51977392f1192b6b4f77b", - "meta_info.json:md5,cd51b8bedbafdc0123db4db59d2aaf7d", - "meta_info.json:md5,4bdc7b4d03bc6b4704eb04d89f9c36af", - "meta_info.json:md5,c1aabb3eb6a845eb578f222e6af48ae5", - "meta_info.json:md5,f606b889a0f98b4cf79cf2b5f1f9a9a5", - "meta_info.json:md5,707c0167c7800abf1a12b8f4437e4bfb", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_dupradar-section-plot.txt:md5,1bb6be44bf23ba406d1a44412eb255f5", - "multiqc_fail_strand_check_table.txt:md5,b73dd03ea0a10e270b1c7ff8871c38ba", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "multiqc_general_stats.txt:md5,9697b7b40b6852b095a990ce432d82e1", - "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", - "multiqc_rseqc_bam_stat.txt:md5,1aa9eeb5b9d283ba77e98f0f5ea0f712", - "multiqc_rseqc_infer_experiment.txt:md5,475b85d8065528e9674a74d2d43644ab", - "multiqc_rseqc_junction_annotation.txt:md5,e78e23f7f32cc2c58136df6ed89d7638", - "multiqc_rseqc_read_distribution.txt:md5,b7106d48346fe4150a8094ef1744f8b3", - "multiqc_salmon.txt:md5,daed924a3d9ba8d9bf35bad9d4ec07f9", - "multiqc_salmon_deseq2_clustering-plot.txt:md5,cf7bf557dfdcde533c599c435f566dce", - "multiqc_salmon_deseq2_clustering-plot_1.txt:md5,0685e6840b85aa4b36e1e3622bc91e4a", - "multiqc_salmon_deseq2_clustering-plot_2.txt:md5,90c0c2745c295fcc0a2fb9218281bec9", - "multiqc_salmon_deseq2_clustering-plot_3.txt:md5,ee5baadfcb9a9bbf375dc08fa6998b1c", - "multiqc_salmon_deseq2_clustering-plot_4.txt:md5,aa48c14dae0bcf9ee6b3f88142b156cb", - "multiqc_salmon_deseq2_pca-plot.txt:md5,301050113f8d404171c962f685d5b10b", - "multiqc_samtools_flagstat.txt:md5,c73d1a59c0c9e3a496e092cc4999ad6d", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "multiqc_samtools_stats.txt:md5,8f0c8097d48301461ac419cbf40b56b0", - "multiqc_star.txt:md5,ae82337a5f847c86e8ffe14e04dfeaee", - "multiqc_star_salmon_deseq2_clustering-plot.txt:md5,72d5b6d429709160351d875524a50a7c", - "multiqc_star_salmon_deseq2_clustering-plot_1.txt:md5,37a19cbfb14a04455b57b6160d4ef25e", - "multiqc_star_salmon_deseq2_clustering-plot_2.txt:md5,ebad3b29617432485579000fb421958b", - "multiqc_star_salmon_deseq2_clustering-plot_3.txt:md5,0623170a882f18ef18387da6df69a650", - "multiqc_star_salmon_deseq2_clustering-plot_4.txt:md5,ebaa497884793b38eef593d98516ecc9", - "multiqc_star_salmon_deseq2_pca-plot.txt:md5,be897cdf8bba2b37249925f42a3dceae", - "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,02044ed1bf1eca19a8a87c9971cdc049", "qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa", - "qualimap_genomic_origin.txt:md5,bf9f1cba02195a298fb54c984c3269a6", "qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce", - "qualimap_rnaseq_genome_results.txt:md5,ce5f4f7f5afa8f1e5666f738c4f414e7", - "rnaseq_qc_results.txt:md5,6bb8c2b18eb67b015bba7d92944cd687", - "rnaseq_qc_results.txt:md5,3eed764ef657161586b04670aad512d6", - "rnaseq_qc_results.txt:md5,401d4141bd4d884b35faa4cb497311f7", - "rnaseq_qc_results.txt:md5,fdf42ac95316d03a8ed66ab87d1b3d23", - "rnaseq_qc_results.txt:md5,9c6543bf977cea9624aab0d2c0eb2640", - "rseqc_bam_stat.txt:md5,ba2575875efaf137f8bf7c2b790d5b1b", "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", - "rseqc_inner_distance.txt:md5,19c55be80264821100f270661ac4937f", - "rseqc_inner_distance_plot_Counts.txt:md5,b8116ab4d78349e72a5d2ee3ca22597c", - "rseqc_inner_distance_plot_Percentages.txt:md5,2a9506bb04f2b661de081795cff17f46", - "rseqc_junction_annotation_junctions_plot_Events.txt:md5,90f1fabea84aa36f647b980978d01e58", - "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,454eb9917793890ee4837fce43e3a8dd", - "rseqc_junction_saturation_all.txt:md5,59d36ebefa6ea9568dadb8631a9325a7", - "rseqc_junction_saturation_plot_All_Junctions.txt:md5,28cdbb3a7bf6b52b39ad7e16f5df48ca", - "rseqc_junction_saturation_plot_Known_Junctions.txt:md5,e9be5dd2857abb8a15154b8435ecb915", - "rseqc_junction_saturation_plot_Novel_Junctions.txt:md5,35ebc2ccd7b77a51c7fff5ab9ea9d96c", - "rseqc_read_distribution_plot.txt:md5,48cea394a38d0f0ed3044b0a54638e65", - "rseqc_read_dups.txt:md5,28180affc24fcd67eda69be83d0825d2", - "rseqc_read_dups_plot.txt:md5,a9f437a3a7eaeb2709fa63644de16ea0", - "salmon.merged.gene_counts.tsv:md5,c14cab7e15cfac73ec0602dc2c404551", - "salmon.merged.gene_counts.tsv:md5,52bf9bce9175a6158b38f6dda338ad95", - "salmon.merged.gene_counts_length_scaled.tsv:md5,45ebc7b36ba8078aecd0fa187ea7f289", - "salmon.merged.gene_counts_length_scaled.tsv:md5,c3c6d4844e2d3e3edb77fd59d992d463", - "salmon.merged.gene_counts_scaled.tsv:md5,a6081c816f2476be1a8f25c6b569a441", - "salmon.merged.gene_counts_scaled.tsv:md5,31f3879878aa8157a04de604d650d0a2", - "salmon.merged.gene_lengths.tsv:md5,f45995c98ed1c30da09d1387c10b9480", - "salmon.merged.gene_lengths.tsv:md5,fbf847cbf9a23eb9b203c64ee209d5f1", - "salmon.merged.gene_tpm.tsv:md5,53a07196cb7b323f086a1f0e494ab929", - "salmon.merged.gene_tpm.tsv:md5,634b52e5978685de75abbf0cfb8b3b1e", - "salmon.merged.transcript_counts.tsv:md5,ff0f5be09ca7a322672c0074ba35da17", - "salmon.merged.transcript_counts.tsv:md5,ec4c48f1b1072a0e8e943e709c00e189", - "salmon.merged.transcript_lengths.tsv:md5,34c408ef2a80fbcd386c998bedaeca71", - "salmon.merged.transcript_lengths.tsv:md5,104b660bec01e6e014e21c2de239164e", - "salmon.merged.transcript_tpm.tsv:md5,c5786607417d24a0edd9c35c84b9d5e7", - "salmon.merged.transcript_tpm.tsv:md5,32961510c67426541f3729cd565ba5ab", - "salmon_plot.txt:md5,83ee202f66071102f1f7b5ae5c02f872", - "samtools-flagstat-dp_Percentage_of_total.txt:md5,fb2847aa158ce48ffd9fdd256afca29a", - "samtools-flagstat-dp_Read_counts.txt:md5,8de72682470e02ffab7362ec5b603fab", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", - "samtools-stats-dp.txt:md5,5f43f4096834e64f009d614b9e3aa9f3", - "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", - "star_alignment_plot.txt:md5,a44811c928719507cee0f98da7492fd1", - "star_summary_table.txt:md5,32aab6812d43f3c850b739eda99990f1", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] @@ -1518,6 +1363,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T11:17:15.946467" + "timestamp": "2024-09-13T17:49:03.61297" } } \ No newline at end of file diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 7bc3666ce..69931c964 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -82,21 +82,14 @@ "trimgalore" ], [ - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T11:24:11.569217" + "timestamp": "2024-09-13T17:55:33.048993" }, "Params: --aligner hisat2": { "content": [ @@ -1175,83 +1168,36 @@ "xls" ], [ - "RAP1_IAA_30M_REP1.bam_stat.txt:md5,b38becac2242c9e565453a3147a3679e", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,079b099e5c5e9fe5e2559dfc938aa48b", 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"rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,d233f89c3c69a0dfc2e66d4d5b8c7ea1", - "rseqc_junction_saturation_all.txt:md5,834981a3b3c2fb65e87883fb16c6a875", - "rseqc_junction_saturation_plot_All_Junctions.txt:md5,25467839fa2f94069ec67d3b46ddf7e9", - "rseqc_junction_saturation_plot_Known_Junctions.txt:md5,f18ba2fe3ab1a6b563aa4c4b11c5b0f8", - "rseqc_junction_saturation_plot_Novel_Junctions.txt:md5,35acb39867cae9e5e3df216f8e2af9a4", - "rseqc_read_distribution_plot.txt:md5,243e8358c7cb5a13d99f715c70c624cb", - "rseqc_read_dups.txt:md5,e79a116d76176f9e18532544a1f20ec4", - "rseqc_read_dups_plot.txt:md5,ed6a2aef667b65f49129c2af874fdbb5", - "salmon.merged.gene_counts.tsv:md5,c14cab7e15cfac73ec0602dc2c404551", - "salmon.merged.gene_counts_length_scaled.tsv:md5,b222b5c1faea3c464a1fe446cd4388ad", - "salmon.merged.gene_counts_scaled.tsv:md5,a210d2b06950b8d4ba1312509a028e18", - "salmon.merged.gene_lengths.tsv:md5,8f36e625921efbd23d0bcb57d353de9d", - "salmon.merged.gene_tpm.tsv:md5,dcd903f695d97a46d4b98215b48faeea", - "salmon.merged.transcript_counts.tsv:md5,ff0f5be09ca7a322672c0074ba35da17", - "salmon.merged.transcript_lengths.tsv:md5,81da7b0f0b61ee9ca23615d2c8b9a84e", - "salmon.merged.transcript_tpm.tsv:md5,b6986d60eaafcdacabca50d78e76f107", - "salmon_plot.txt:md5,59ee362906ef224982a20f32a2617c48", - "samtools-flagstat-dp_Percentage_of_total.txt:md5,edfac448e9dcd51f2bb11a84ca0c1be2", - "samtools-flagstat-dp_Read_counts.txt:md5,22647a049eebf1d595ebae3c67361ba1", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3625f666cc09d0f07990716aeccd869f", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,6c323b383a6506d124506405b9463d93", - "samtools-stats-dp.txt:md5,b50cdd0dfe9fedcdeb3f79477ef5180f", - "samtools_alignment_plot.txt:md5,b6ba3cc94a91b3d0a84c3fa721914744", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], @@ -1398,6 +1277,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T11:23:27.694279" + "timestamp": "2024-09-13T17:54:49.218047" } } \ No newline at end of file diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index ceffc6ab0..524118315 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -226,22 +226,9 @@ "tx2gene.tsv" ], [ - "RAP1_IAA_30M_REP1.stats.txt:md5,a87292c6f7166096166a9015c2e63dac", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,cdb7d4cd19558158c86c9cfc17f6d9b7", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,3031e78f567f2d21278eb633cf5d4830", - "RAP1_UNINDUCED_REP1.stats.txt:md5,781e49024150a8313779c574b58ad035", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,a4382128973b6dbcbcc9c3cc7263a6e8", - "RAP1_UNINDUCED_REP2.stats.txt:md5,e455d0163bf2d988224b0c0092605213", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,91604d61bbc72d4c38df8331cd835ef3", - "WT_REP1.stats.txt:md5,6eab6936804c1157d5e1c61c0562d7de", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,f99a0bef8bfad292319b3455a71342e3", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,05260ac3d28c148398d2ae2da98a1c2e", - "WT_REP2.stats.txt:md5,f6df7d4d9a5b553209f31dec2a30f92b", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,ff437dfc6744a844c412593078fcc593", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,5cfdbef1faeb38d9b7e7767fdf19d4df", - "abundance.tsv:md5,d781d4480dc636c8a3b6aa300ac184a2", + "abundance.tsv:md5,a208e4943f6efb704f68463df3147a49", "abundance.tsv:md5,6fd77021287360f5005c90807233ab23", - "abundance.tsv:md5,6fb211dc8e4fd238ca68d21d6cc83cf5", + "abundance.tsv:md5,602da7c00d92c1f21905d1a316c4286b", "abundance.tsv:md5,b6ae4ef44f718a789f58dc6451b6eebb", "abundance.tsv:md5,a2c6108c384662f4da8c7b7fe8f27e02", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", @@ -257,26 +244,24 @@ "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c", "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "fastqc_top_overrepresented_sequences_table.txt:md5,6ef1543c6c128d51cc2b702a96c7ef63", - "kallisto.merged.gene_counts.tsv:md5,70b5a70a847e2469a3fb3b1ea4886966", - "kallisto.merged.gene_counts_length_scaled.tsv:md5,9b85077c766afe71785eb015b09d5a78", - "kallisto.merged.gene_counts_scaled.tsv:md5,85e383eff98eedbc678175c8aa873ab0", - "kallisto.merged.gene_lengths.tsv:md5,cf249fee85862c2df5a4f76244d6f701", - "kallisto.merged.gene_tpm.tsv:md5,baae791ff46f457056571b6923843c28", - "kallisto.merged.transcript_counts.tsv:md5,85d11e775aab1bba3c0c5afc97c57129", - "kallisto.merged.transcript_lengths.tsv:md5,4f13d812e9eb8b4d85d12b0721d7a37d", - "kallisto.merged.transcript_tpm.tsv:md5,89a1d81d93c9dbebdba55e28b52d6ac2", + "kallisto.merged.gene_counts.tsv:md5,8813a72fee7acc6683681adcd9c3205d", + "kallisto.merged.gene_counts_length_scaled.tsv:md5,385855f0371d9b09f5929943d0bd3c5c", + "kallisto.merged.gene_counts_scaled.tsv:md5,384a713001db2273d4aa6a0b5a365f88", + "kallisto.merged.gene_lengths.tsv:md5,360be233f67438b3c74b30d4ffb82217", + "kallisto.merged.gene_tpm.tsv:md5,1c757b30cf764af3021536ed58929b47", + "kallisto.merged.transcript_counts.tsv:md5,12b42da001ba7217d84158bfc1dafb93", + "kallisto.merged.transcript_lengths.tsv:md5,efb283191ff876ea179db50bfd67e1e8", + "kallisto.merged.transcript_tpm.tsv:md5,f4b96383c1270f734ff291e6cddfcb72", "kallisto_alignment.txt:md5,fafc53710b8d3cd6d3e456a1bd8c30e0", "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "multiqc_general_stats.txt:md5,081a8c7890b8c68da5fcf88509b09648", - "multiqc_kallisto.txt:md5,48b29e88fbb64db2069316c6c2f662c3", - "run_info.json:md5,2f054b3d7acf563f7c22c006dea7f206", - "run_info.json:md5,51bc7adda1942a208b9bdee9bf9214e4", - "run_info.json:md5,5fa89f779d412f60cb022615bf22d93c", - "run_info.json:md5,a475f356826703868f8d7ed21124babf", - "run_info.json:md5,1ddaaf80c06118def7bf6f374ac10b86", + "multiqc_kallisto.txt:md5,6fae2082e277bdea611a80f98e124165", + "run_info.json:md5,309ff0ae944127e8b6791e76ac196a01", + "run_info.json:md5,ccf4a5962415c6f1adb6e7ae05c4b86c", + "run_info.json:md5,8d2d93f6a5c27b11d3e428f628385bb7", + "run_info.json:md5,d12554278f74e04f7e6614a8f6f0f3dd", + "run_info.json:md5,019d3f1b7684c2e153be759cbc388b8b", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], @@ -284,7 +269,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T11:27:10.252249" + "timestamp": "2024-09-13T18:00:22.935935" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ @@ -351,20 +336,13 @@ "trimgalore" ], [ - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T11:28:04.202471" + "timestamp": "2024-09-13T18:04:31.974316" } } \ No newline at end of file diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index 131b0f0a0..0da4ccde3 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -27,24 +27,353 @@ class UTILS { static List exclusionRegexesForUnstableFileContents = [ // To exclude files with timestamps in the format YYYY-MM-DD_HH-MM-SS /\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}/, - // To exclude "goleft_indexcov-bin-plot.txt" - /goleft_indexcov-bin-plot\.txt/, - // To exclude "multiqc_data.json" + + // To exlude bbsplit files + /.*\.stats\.txt/, + + // To exclude fastqc files + /.*_fastqc\.html/, + /.*_fastqc\.zip/, + + // To exclude from the MultiQC reports + /cutadapt_filtered_reads_plot-cnt\.pdf/, + /cutadapt_filtered_reads_plot-cnt\.svg/, + /cutadapt_filtered_reads_plot-pct\.pdf/, + /cutadapt_filtered_reads_plot-pct\.svg/, + /cutadapt_trimmed_sequences_plot_3_Counts\.pdf/, + /cutadapt_trimmed_sequences_plot_3_Counts\.svg/, + /cutadapt_trimmed_sequences_plot_3_Obs_Exp\.pdf/, + /cutadapt_trimmed_sequences_plot_3_Obs_Exp\.svg/, + /dupradar-section-plot\.pdf/, + /dupradar-section-plot\.svg/, + /fail_strand_check_table\.pdf/, + /fail_strand_check_table\.png/, + /fail_strand_check_table\.svg/, + /fastqc-status-check-heatmap-1\.pdf/, + /fastqc-status-check-heatmap-1\.svg/, + /fastqc-status-check-heatmap\.pdf/, + /fastqc-status-check-heatmap\.svg/, + /fastqc_adapter_content_plot\.pdf/, + /fastqc_adapter_content_plot\.png/, + /fastqc_adapter_content_plot\.svg/, + /fastqc_overrepresented_sequences_plot-1\.pdf/, + /fastqc_overrepresented_sequences_plot-1\.svg/, + /fastqc_overrepresented_sequences_plot\.pdf/, + /fastqc_overrepresented_sequences_plot\.svg/, + /fastqc_per_base_n_content_plot-1\.pdf/, + /fastqc_per_base_n_content_plot-1\.png/, + /fastqc_per_base_n_content_plot-1\.svg/, + /fastqc_per_base_n_content_plot\.pdf/, + /fastqc_per_base_n_content_plot\.png/, + /fastqc_per_base_n_content_plot\.svg/, + /fastqc_per_base_sequence_quality_plot-1\.pdf/, + /fastqc_per_base_sequence_quality_plot-1\.png/, + /fastqc_per_base_sequence_quality_plot-1\.svg/, + /fastqc_per_base_sequence_quality_plot\.pdf/, + /fastqc_per_base_sequence_quality_plot\.png/, + /fastqc_per_base_sequence_quality_plot\.svg/, + /fastqc_per_sequence_gc_content_plot-1_Counts\.pdf/, + /fastqc_per_sequence_gc_content_plot-1_Counts\.svg/, + /fastqc_per_sequence_gc_content_plot-1_Percentages\.pdf/, + /fastqc_per_sequence_gc_content_plot-1_Percentages\.svg/, + /fastqc_per_sequence_gc_content_plot_Counts\.pdf/, + /fastqc_per_sequence_gc_content_plot_Counts\.svg/, + /fastqc_per_sequence_gc_content_plot_Percentages\.pdf/, + /fastqc_per_sequence_gc_content_plot_Percentages\.svg/, + /fastqc_per_sequence_quality_scores_plot-1\.pdf/, + /fastqc_per_sequence_quality_scores_plot-1\.svg/, + /fastqc_per_sequence_quality_scores_plot\.pdf/, + /fastqc_per_sequence_quality_scores_plot\.svg/, + /fastqc_sequence_counts_plot-1-cnt\.pdf/, + /fastqc_sequence_counts_plot-1-cnt\.svg/, + /fastqc_sequence_counts_plot-1-pct\.pdf/, + /fastqc_sequence_counts_plot-1-pct\.svg/, + /fastqc_sequence_counts_plot-cnt\.pdf/, + /fastqc_sequence_counts_plot-cnt\.svg/, + /fastqc_sequence_counts_plot-pct\.pdf/, + /fastqc_sequence_counts_plot-pct\.svg/, + /fastqc_sequence_duplication_levels_plot-1\.pdf/, + /fastqc_sequence_duplication_levels_plot-1\.svg/, + /fastqc_sequence_duplication_levels_plot\.pdf/, + /fastqc_sequence_duplication_levels_plot\.svg/, + /fastqc_sequence_length_distribution_plot\.pdf/, + /fastqc_sequence_length_distribution_plot\.png/, + /fastqc_sequence_length_distribution_plot\.svg/, + /fastqc_top_overrepresented_sequences_table-1\.pdf/, + /fastqc_top_overrepresented_sequences_table-1\.png/, + /fastqc_top_overrepresented_sequences_table-1\.svg/, + /fastqc_top_overrepresented_sequences_table-1\.txt/, + /fastqc_top_overrepresented_sequences_table\.pdf/, + /fastqc_top_overrepresented_sequences_table\.png/, + /fastqc_top_overrepresented_sequences_table\.svg/, + /fastqc_top_overrepresented_sequences_table\.txt/, + /featurecounts_biotype_plot-cnt\.pdf/, + /featurecounts_biotype_plot-cnt\.svg/, + /featurecounts_biotype_plot-pct\.pdf/, + /featurecounts_biotype_plot-pct\.svg/, + /general_stats_table\.pdf/, + /general_stats_table\.png/, + /general_stats_table\.svg/, + /junction_saturation_known\.txt/, + /junction_saturation_novel\.txt/, /multiqc_data\.json/, - // To exclude "multiqc_sources.txt" + /multiqc_dupradar-section-plot\.txt/, + /multiqc_fail_strand_check_table\.txt/, + /multiqc_general_stats\.txt/, + /multiqc_picard_dups\.txt/, + /multiqc_report.html/, + /multiqc_rseqc_bam_stat\.txt/, + /multiqc_rseqc_infer_experiment\.txt/, + /multiqc_rseqc_junction_annotation\.txt/, + /multiqc_rseqc_read_distribution\.txt/, + /multiqc_salmon\.txt/, + /multiqc_salmon_deseq2_clustering-plot\.txt/, + /multiqc_salmon_deseq2_clustering-plot_.*\.txt/, + /multiqc_salmon_deseq2_pca-plot\.txt/, + /multiqc_samtools_flagstat\.txt/, + /multiqc_samtools_stats\.txt/, + /multiqc_software_versions\.txt/, /multiqc_sources\.txt/, + /multiqc_star\.txt/, + /multiqc_star_salmon_deseq2_clustering-plot\.txt/, + /multiqc_star_salmon_deseq2_clustering-plot_.*\.txt/, + /multiqc_star_salmon_deseq2_pca-plot\.txt/, + /picard_deduplication-cnt\.pdf/, + /picard_deduplication-cnt\.png/, + /picard_deduplication-cnt\.svg/, + /picard_deduplication-pct\.pdf/, + /picard_deduplication-pct\.png/, + /picard_deduplication-pct\.svg/, + /picard_deduplication\.txt/, + /qualimap_gene_coverage_profile_Counts\.pdf/, + /qualimap_gene_coverage_profile_Counts\.svg/, + /qualimap_gene_coverage_profile_Normalised\.pdf/, + /qualimap_gene_coverage_profile_Normalised\.svg/, + /qualimap_genomic_origin-cnt\.pdf/, + /qualimap_genomic_origin-cnt\.png/, + /qualimap_genomic_origin-cnt\.svg/, + /qualimap_genomic_origin-pct\.pdf/, + /qualimap_genomic_origin-pct\.png/, + /qualimap_genomic_origin-pct\.svg/, + /qualimap_genomic_origin\.txt/, + /qualimap_rnaseq_genome_results\.txt/, + /rseqc_bam_stat\.pdf/, + /rseqc_bam_stat\.png/, + /rseqc_bam_stat\.svg/, + /rseqc_bam_stat\.txt/, + /rseqc_infer_experiment_plot\.pdf/, + /rseqc_infer_experiment_plot\.svg/, + /rseqc_inner_distance\.txt/, + /rseqc_inner_distance_plot_Counts\.pdf/, + /rseqc_inner_distance_plot_Counts\.png/, + /rseqc_inner_distance_plot_Counts\.svg/, + /rseqc_inner_distance_plot_Counts\.txt/, + /rseqc_inner_distance_plot_Percentages\.pdf/, + /rseqc_inner_distance_plot_Percentages\.png/, + /rseqc_inner_distance_plot_Percentages\.svg/, + /rseqc_inner_distance_plot_Percentages\.txt/, + /rseqc_junction_annotation_junctions_plot_Events-cnt\.pdf/, + /rseqc_junction_annotation_junctions_plot_Events-cnt\.png/, + /rseqc_junction_annotation_junctions_plot_Events-cnt\.svg/, + /rseqc_junction_annotation_junctions_plot_Events-pct\.pdf/, + /rseqc_junction_annotation_junctions_plot_Events-pct\.png/, + /rseqc_junction_annotation_junctions_plot_Events-pct\.svg/, + /rseqc_junction_annotation_junctions_plot_Events\.txt/, + /rseqc_junction_annotation_junctions_plot_Junctions-cnt\.pdf/, + /rseqc_junction_annotation_junctions_plot_Junctions-cnt\.png/, + /rseqc_junction_annotation_junctions_plot_Junctions-cnt\.svg/, + /rseqc_junction_annotation_junctions_plot_Junctions-pct\.pdf/, + /rseqc_junction_annotation_junctions_plot_Junctions-pct\.png/, + /rseqc_junction_annotation_junctions_plot_Junctions-pct\.svg/, + /rseqc_junction_annotation_junctions_plot_Junctions\.txt/, + /rseqc_junction_saturation_all\.txt/, + /rseqc_junction_saturation_plot_All_Junctions\.pdf/, + /rseqc_junction_saturation_plot_All_Junctions\.png/, + /rseqc_junction_saturation_plot_All_Junctions\.svg/, + /rseqc_junction_saturation_plot_All_Junctions\.txt/, + /rseqc_junction_saturation_plot_Known_Junctions\.pdf/, + /rseqc_junction_saturation_plot_Known_Junctions\.png/, + /rseqc_junction_saturation_plot_Known_Junctions\.svg/, + /rseqc_junction_saturation_plot_Known_Junctions\.txt/, + /rseqc_junction_saturation_plot_Novel_Junctions\.pdf/, + /rseqc_junction_saturation_plot_Novel_Junctions\.png/, + /rseqc_junction_saturation_plot_Novel_Junctions\.svg/, + /rseqc_junction_saturation_plot_Novel_Junctions\.txt/, + /rseqc_read_distribution_plot-cnt\.pdf/, + /rseqc_read_distribution_plot-cnt\.png/, + /rseqc_read_distribution_plot-cnt\.svg/, + /rseqc_read_distribution_plot-pct\.pdf/, + /rseqc_read_distribution_plot-pct\.png/, + /rseqc_read_distribution_plot-pct\.svg/, + /rseqc_read_distribution_plot\.txt/, + /rseqc_read_dups\.txt/, + /rseqc_read_dups_plot\.pdf/, + /rseqc_read_dups_plot\.svg/, + /rseqc_read_dups_plot\.txt/, + /salmon_deseq2_clustering-plot\.pdf/, + /salmon_deseq2_clustering-plot\.png/, + /salmon_deseq2_clustering-plot\.svg/, + /salmon_deseq2_pca-plot\.pdf/, + /salmon_deseq2_pca-plot\.png/, + /salmon_deseq2_pca-plot\.svg/, + /salmon_plot\.pdf/, + /salmon_plot\.png/, + /salmon_plot\.svg/, + /salmon_plot\.txt/, + /samtools-flagstat-dp_Percentage_of_total\.pdf/, + /samtools-flagstat-dp_Percentage_of_total\.png/, + /samtools-flagstat-dp_Percentage_of_total\.svg/, + /samtools-flagstat-dp_Percentage_of_total\.txt/, + /samtools-flagstat-dp_Read_counts\.pdf/, + /samtools-flagstat-dp_Read_counts\.png/, + /samtools-flagstat-dp_Read_counts\.svg/, + /samtools-flagstat-dp_Read_counts\.txt/, + /samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt\.pdf/, + /samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt\.svg/, + /samtools-idxstats-mapped-reads-plot_Normalised_Counts-log\.pdf/, + /samtools-idxstats-mapped-reads-plot_Normalised_Counts-log\.svg/, + /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt\.pdf/, + /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt\.svg/, + /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log\.pdf/, + /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log\.svg/, + /samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt\.pdf/, + /samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt\.svg/, + /samtools-idxstats-mapped-reads-plot_Raw_Counts-log\.pdf/, + /samtools-idxstats-mapped-reads-plot_Raw_Counts-log\.svg/, + /samtools-stats-dp\.pdf/, + /samtools-stats-dp\.png/, + /samtools-stats-dp\.svg/, + /samtools-stats-dp\.txt/, + /samtools_alignment_plot-cnt\.pdf/, + /samtools_alignment_plot-cnt\.png/, + /samtools_alignment_plot-cnt\.svg/, + /samtools_alignment_plot-pct\.pdf/, + /samtools_alignment_plot-pct\.png/, + /samtools_alignment_plot-pct\.svg/, + /samtools_alignment_plot\.txt/, + /star_alignment_plot-cnt\.pdf/, + /star_alignment_plot-cnt\.png/, + /star_alignment_plot-cnt\.svg/, + /star_alignment_plot-pct\.pdf/, + /star_alignment_plot-pct\.png/, + /star_alignment_plot-pct\.svg/, + /star_alignment_plot\.txt/, + /star_salmon_deseq2_clustering-plot\.pdf/, + /star_salmon_deseq2_clustering-plot\.png/, + /star_salmon_deseq2_clustering-plot\.svg/, + /star_salmon_deseq2_pca-plot\.pdf/, + /star_salmon_deseq2_pca-plot\.png/, + /star_salmon_deseq2_pca-plot\.svg/, + /star_summary_table\.pdf/, + /star_summary_table\.png/, + /star_summary_table\.svg/, + /star_summary_table\.txt/, + + // To exclude from deseq2_qc + /RAP1_IAA_30M_REP1\.txt/, + /RAP1_UNINDUCED_REP1\.txt/, + /RAP1_UNINDUCED_REP2\.txt/, + /WT_REP1\.txt/, + /WT_REP2\.txt/, + /deseq2\.dds\.RData/, + /deseq2\.pca\.vals\.txt/, + /deseq2\.plots\.pdf/, + /deseq2\.sample\.dists\.txt/, + /deseq2\.size_factors\.RData/, + + // To exclude from salmon quant + /fld\.gz/, + /meta_info\.json/, + /flenDist\.txt/, + /salmon_quant\.log/, + /quant\.genes\.sf/, + /quant\.sf/, + + // To exclude from salmon + /salmon\.merged\.gene_counts\.SummarizedExperiment\.rds/, + /salmon\.merged\.gene_counts\.tsv/, + /salmon\.merged\.gene_counts_length_scaled\.SummarizedExperiment\.rds/, + /salmon\.merged\.gene_counts_length_scaled\.tsv/, + /salmon\.merged\.gene_counts_scaled\.SummarizedExperiment\.rds/, + /salmon\.merged\.gene_counts_scaled\.tsv/, + /salmon\.merged\.gene_lengths\.tsv/, + /salmon\.merged\.gene_tpm\.tsv/, + /salmon\.merged\.transcript_counts\.SummarizedExperiment\.rds/, + /salmon\.merged\.transcript_counts\.tsv/, + /salmon\.merged\.transcript_lengths\.tsv/, + /salmon\.merged\.transcript_tpm\.tsv/, + + // To exclude bigwig + /.*\.forward\.bigWig/, + /.*\.reverse\.bigWig/, + + // To exlude dupradar + /.*_duprateExpBoxplot\.pdf/, + /.*_expressionHist\.pdf/, + /.*_duprateExpDens\.pdf/, + + // To exclude featurecounts + /.*\.featureCounts\.txt\.summary/, + + // To exclude star salmon + /.*\.Log\.final\.out/, + /.*\.Log\.out/, + /.*\.Log\.progress\.out/, + + // To exclude Picard Markduplicates metrics + /.*\.markdup\.sorted\.MarkDuplicates\.metrics\.txt/, + + // To exclude Qualimap files + /Junction\sAnalysis\.png/, + /Reads\sGenomic\sOrigin\.png/, + /qualimapReport\.html/, + /rnaseq_qc_results\.txt/, + + // To exclude rseqc + /.*\.DupRate_plot\.pdf/, + /.*\.DupRate_plot\.r/, + /.*\.inner_distance\.txt/, + /.*\.inner_distance_freq\.txt/, + /.*\.inner_distance_mean\.txt/, + /.*\.inner_distance_plot\.pdf/, + /.*\.inner_distance_plot\.r/, + /.*\.junction\.Interact\.bed/, + /.*\.junction\.bed/, + /.*\.junction\.xls/, + /.*\.junctionSaturation_plot\.pdf/, + /.*\.junctionSaturation_plot\.r/, + /.*\.junction_annotation\.log/, + /.*\.junction_plot\.r/, + /.*\.pos\.DupRate\.xls/, + /.*\.read_distribution\.txt/, + /.*\.seq\.DupRate\.xls/, + /.*\.splice_events\.pdf/, + /.*\.splice_junction\.pdf/, + /.*\.bam_stat\.txt/, + + // To exclude from samtools stats + /.*\.markdup\.sorted\.bam\.flagstat/, + /.*\.markdup\.sorted\.bam\.idxstats/, + /.*\.markdup\.sorted\.bam\.stats/, + /.*\.sorted\.bam\.flagstat/, + /.*\.sorted\.bam\.idxstats/, + /.*\.sorted\.bam\.stats/, + + // To exclude from stringtie + /t_data\.ctab/, + /.*\.coverage\.gtf/, + /.*\.gene\.abundance\.txt/, + /.*\.transcripts\.gtf/, + + // To exclude markdup + /.*\.markdup\.sorted\.bam/, + /.*\.markdup\.sorted\.bam\.bai/, + + // To exclude trimgalore + /.*\.fastq\.gz_trimming_report\.txt/, + // To exclude params files with timestamps - /params_\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}\.json/, - // To exclude "*.deduped.cram.metrics.multiqc.tsv" - /.*\.deduped\.cram\.metrics\.multiqc\.tsv/, - // To exclude "goleft_bin.txt" - /goleft_bin\.txt/, - // To exclude "goleft_roc.txt" - /goleft_roc\.txt/, - // To exclude any "multiqc_sample*.txt" files - /multiqc_sample.*\.txt/, - // To exclude "multiqc_software_versions.txt" - /multiqc_software_versions\.txt/ + /params_\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}\.json/ ] } From 29af9969a2761143b9764661cbf7a2f897350132 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Sep 2024 19:01:43 +0200 Subject: [PATCH 039/100] more snapshots --- tests/lib/UTILS.groovy | 8 ++ tests/min_mapped_reads.nf.test.snap | 145 +------------------------ tests/remove_ribo_rna.nf.test.snap | 161 +--------------------------- tests/salmon.nf.test.snap | 48 +-------- tests/skip_qc.nf.test.snap | 87 +-------------- tests/skip_trimming.nf.test.snap | 141 +----------------------- tests/star_rsem.nf.test.snap | 140 ++---------------------- 7 files changed, 27 insertions(+), 703 deletions(-) diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index 0da4ccde3..c3910ca17 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -28,6 +28,14 @@ class UTILS { // To exclude files with timestamps in the format YYYY-MM-DD_HH-MM-SS /\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}/, + // Stable files, but order is changing + /ambig_info\.tsv/, + /cmd_info\.json/, + /coverage_profile_along_genes_(high)\.txt/, + /coverage_profile_along_genes_(low)\.txt/, + /coverage_profile_along_genes_(total)\.txt/, + /lib_format_counts\.json/, + // To exlude bbsplit files /.*\.stats\.txt/, diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 4aa9488c4..004091643 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -1039,62 +1039,24 @@ "xls" ], [ - "RAP1_IAA_30M_REP1.bam_stat.txt:md5,b882e444c89be4ceed80e29865166b1a", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,f3688a214d33a43ad79abe4b31df0c4b", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.txt:md5,b38da3230d4d29ebc8d4af36852d7212", - "RAP1_IAA_30M_REP1.gene.abundance.txt:md5,f9d863eb7c592dae0a150bb75e6dfb11", "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,169d25b95c008bebe9ce886fea6a4e33", - "RAP1_IAA_30M_REP1.inner_distance.txt:md5,5c15c31ba27e6be7c54f5c442e2fe22f", - "RAP1_IAA_30M_REP1.inner_distance_freq.txt:md5,0d3b00e36f5afa9c058fb3a99a5d9dcf", - "RAP1_IAA_30M_REP1.inner_distance_mean.txt:md5,002a82a3fb9fe6eb58e2dce854a5922f", - "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt:md5,e8f0ca1dedbaff4a252d7a04eac184e5", - "RAP1_IAA_30M_REP1.read_distribution.txt:md5,a181a8045a4aaee911e6acd60cc25d43", - "RAP1_IAA_30M_REP1.stats.txt:md5,a87292c6f7166096166a9015c2e63dac", - "RAP1_IAA_30M_REP1.txt:md5,070ac8e0dd225793901887863446798d", - "RAP1_IAA_30M_REP1.txt:md5,c9edfeadc7fb5111837101a81af1c87e", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,63a376d7309c2ab1efa326c7090af97c", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,11193ea7912ace165dbd50f33e74063c", - "RAP1_UNINDUCED_REP1.bam_stat.txt:md5,d00442929f8a18945d4597167fe3bb6d", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,d241d50e582ceb97e6f16b3556f5f5a9", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,2ab175746532de1c54020c1eabc27bb5", - "RAP1_UNINDUCED_REP1.gene.abundance.txt:md5,43d91c4bd7de0dce0bd4c55a107b15f3", "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,2ca0ce0fd3204bd2cc4812c4655b1f1f", - "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt:md5,36c06309c22095a4eccdb397a7da2567", - "RAP1_UNINDUCED_REP1.read_distribution.txt:md5,1d91e11972e9b0a55035f4d9b2fa9b86", - "RAP1_UNINDUCED_REP1.stats.txt:md5,781e49024150a8313779c574b58ad035", - "RAP1_UNINDUCED_REP1.txt:md5,49927ec2c47a93d48a3bbc62f6289c14", - "RAP1_UNINDUCED_REP1.txt:md5,18a36718e888c138c65f2a6ecd8862a7", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,115224a930071e7826ca3a49437b5294", - "RAP1_UNINDUCED_REP2.bam_stat.txt:md5,447c12933610cb3e0aeb4560906332c6", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,b621ce1e803d8670ece6c66391c33ba4", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,480b2586a878bc22f5b73f94051b41d8", - "RAP1_UNINDUCED_REP2.gene.abundance.txt:md5,1b6cd8a16d7b12f4e0b2da9d008799a6", "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,7d5705880188f9beab1939e08d6b8f40", - "RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt:md5,12e9e5a3e2eb8b7d865f3bf14cd6e9a0", - "RAP1_UNINDUCED_REP2.read_distribution.txt:md5,ece206e073f3410f6e40d2ff91c9a714", - "RAP1_UNINDUCED_REP2.stats.txt:md5,e455d0163bf2d988224b0c0092605213", - "RAP1_UNINDUCED_REP2.txt:md5,a9278cb2b25db32f9f6af60ca8789ca8", - "RAP1_UNINDUCED_REP2.txt:md5,6bd573fd119f84464dfca6044fe41704", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,0ba9aa38aac8309a6bcdf4b612e0c996", - "WT_REP1.stats.txt:md5,6eab6936804c1157d5e1c61c0562d7de", - "WT_REP1.txt:md5,ec8f0bdfaa7bb558c91e0db2679eec8f", - "WT_REP1.txt:md5,118f0ab1b07ae7f4ef0b0bbdf738770d", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,6b514c401970acc5d810aee92a9a40dc", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,90e6921a7ef74e5fac626d762b81554f", - "WT_REP2.stats.txt:md5,f6df7d4d9a5b553209f31dec2a30f92b", - "WT_REP2.txt:md5,3761cdcd554d5b696a42fd83f0f4cab7", - "WT_REP2.txt:md5,c23242f9bc76f5528d17d869554c8d2c", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,bb782f3e6220c1f14d60c41fed0cdff6", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,994e86f685aa8c2283a460f75eb2f9dd", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", @@ -1127,10 +1089,6 @@ "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", - "deseq2.pca.vals.txt:md5,27d34023c7d31086de1ba3197f33dd19", - "deseq2.pca.vals.txt:md5,159d70e157d4273cbf7121a06208a536", - "deseq2.sample.dists.txt:md5,aa500ce0a6060f5b53b8d60ac917cea3", - "deseq2.sample.dists.txt:md5,c27be3cc1cb2f5c6f663dfe7d538eff3", "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", @@ -1151,118 +1109,28 @@ "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "fastqc_top_overrepresented_sequences_table-1.txt:md5,fbd6b1f651b8fbe108b05a19e9ba7ca7", - "fastqc_top_overrepresented_sequences_table.txt:md5,4d35aa1d2dc273c5187185d0afe425be", - "flenDist.txt:md5,20e8a0a7619609c41e1ffcf121d10bf0", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "flenDist.txt:md5,5d954f03ebd5bc0c265055cc3debd150", - "flenDist.txt:md5,301f2d5434bc4d56323fa3dc5ce37d98", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "flenDist.txt:md5,ebc07f9b5676ae11617973a9807a9e09", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "flenDist.txt:md5,f44c42ed199569e78fff56512edaa0f9", - "flenDist.txt:md5,353610ce65c6aadac64f53e90479847d", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "junction_saturation_known.txt:md5,ab5f9521c061e31bbc1106bbd265ee10", - "junction_saturation_novel.txt:md5,fa4ef709f5a8aa1f7b7d3af80ccbbd5f", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", - "meta_info.json:md5,d3afe4bfba459f4c15b0de69939e8380", - "meta_info.json:md5,8670e528b51994976a7fb3325c9281e7", - "meta_info.json:md5,e30483bc3a9a616b759a588fec6c376c", - "meta_info.json:md5,a30aa2293bb7130b6e76415e318ef510", - "meta_info.json:md5,0299b88ec042701532cf680c985d1071", - "meta_info.json:md5,e82420e31ef9a841aba9355abade303e", - "meta_info.json:md5,a2af7e86abab93c089a6fcba9c6dfaa1", - "meta_info.json:md5,4cda47d627c09f4afd9d76e852a6feb8", - "meta_info.json:md5,e269950b8333ef4949b204c20391679e", - "meta_info.json:md5,3fcf53963671c2311ca60df03b486887", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_dupradar-section-plot.txt:md5,dc71a62f9cba9355d3dee15341afe479", "multiqc_fail_mapped_samples_table.txt:md5,5dd9b06f326b1a55d78878343af89927", - "multiqc_fail_strand_check_table.txt:md5,238667d9562ccabf0b5b8c33d41e073a", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,f3c566d2eaf6bf2ffe5ad12036ce3500", - "multiqc_general_stats.txt:md5,84630590d13356a31c4d8956fc312957", - "multiqc_picard_dups.txt:md5,6dff325f1bf12d9de88a11af272be755", - "multiqc_rseqc_bam_stat.txt:md5,1a42760324bbe15d5e099d0392f5db55", - "multiqc_rseqc_infer_experiment.txt:md5,73d3afeb7a97022ae6faf3f57a52f81d", - "multiqc_rseqc_junction_annotation.txt:md5,eaf292e3d11398a65903f46365f763be", - "multiqc_rseqc_read_distribution.txt:md5,52dfe8e95ffb71406c321f06f757bfde", - "multiqc_salmon.txt:md5,dc278b6d85e4ce115c92fe045e0caf86", - "multiqc_salmon_deseq2_clustering-plot.txt:md5,c39fd219828df33259e48aadcdd1997c", - "multiqc_salmon_deseq2_clustering-plot_1.txt:md5,6ccabfcdd11d36e140a7d6615c73ae85", - "multiqc_salmon_deseq2_clustering-plot_2.txt:md5,792ce8a58aefbbd10c0f182fcbc37c7a", - "multiqc_salmon_deseq2_clustering-plot_3.txt:md5,3080d13dee6e437084f27937296ede8a", - "multiqc_salmon_deseq2_clustering-plot_4.txt:md5,c750d2fa8d6dc8a2370335a71d2fa637", - "multiqc_salmon_deseq2_pca-plot.txt:md5,831426c001fe69be0e1ab2bfe32a234b", - "multiqc_samtools_flagstat.txt:md5,ee392f47303185bc9a299bfda8b73c75", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "multiqc_samtools_stats.txt:md5,ae13ad7897ec9421a019c20c42f0ea71", - "multiqc_star.txt:md5,b3dc9dd2d290f12b8835758654a29edd", - "multiqc_star_salmon_deseq2_clustering-plot.txt:md5,72d5b6d429709160351d875524a50a7c", - "multiqc_star_salmon_deseq2_clustering-plot_1.txt:md5,37a19cbfb14a04455b57b6160d4ef25e", - "multiqc_star_salmon_deseq2_clustering-plot_2.txt:md5,ebad3b29617432485579000fb421958b", - "multiqc_star_salmon_deseq2_clustering-plot_3.txt:md5,0623170a882f18ef18387da6df69a650", - "multiqc_star_salmon_deseq2_clustering-plot_4.txt:md5,ebaa497884793b38eef593d98516ecc9", - "multiqc_star_salmon_deseq2_pca-plot.txt:md5,be897cdf8bba2b37249925f42a3dceae", - "picard_deduplication.txt:md5,bcf1670f90e552256db4de7fa65d5306", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,6d377444d29c3d4135980982ab1df2fb", "qualimap_gene_coverage_profile_Normalised.txt:md5,dc8b4f9fddc08e06668f9ee87faac008", - "qualimap_genomic_origin.txt:md5,76988d0ce871eb7190b916bbc4dd5387", "qualimap_rnaseq_cov_hist.txt:md5,a409821701f60811027daef4e7f3ebee", - "qualimap_rnaseq_genome_results.txt:md5,dbaf0e70a31c7606afb2c8b758693d6d", - "rnaseq_qc_results.txt:md5,3eed764ef657161586b04670aad512d6", - "rnaseq_qc_results.txt:md5,fdf42ac95316d03a8ed66ab87d1b3d23", - "rnaseq_qc_results.txt:md5,9c6543bf977cea9624aab0d2c0eb2640", - "rseqc_bam_stat.txt:md5,b468d3e451b9f20b02653df836e56ab7", "rseqc_infer_experiment_plot.txt:md5,749a802379ada3ec9d2083ecbe6aef7e", - "rseqc_inner_distance.txt:md5,554d4ad4dff5154d04dd54283614b8c9", - "rseqc_inner_distance_plot_Counts.txt:md5,7a2a7a5488e742edfb5ec34a699812ea", - "rseqc_inner_distance_plot_Percentages.txt:md5,d3dd88cb4b738fa73affed6d7ba1d9db", - "rseqc_junction_annotation_junctions_plot_Events.txt:md5,7d52ed0ea2a109428249cc835c64fd7f", - "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,b4d76efb9fe0c30418b78dd6c61c42fa", - "rseqc_junction_saturation_all.txt:md5,b6777bbd19f5890f77df68cbdbba3d24", - "rseqc_junction_saturation_plot_All_Junctions.txt:md5,c61c5db0b882c6a8e32d2e04abbcb3b1", - "rseqc_junction_saturation_plot_Known_Junctions.txt:md5,22c5c9647a71ac4d2046f7867fbbcbfe", - "rseqc_junction_saturation_plot_Novel_Junctions.txt:md5,4ede9583a69a35cad23d90ad863bb2c5", - "rseqc_read_distribution_plot.txt:md5,27c914f0530d633c860da6eccba18515", - "rseqc_read_dups.txt:md5,8db51e3a3c2012c65a46a21afbc83a9e", - "rseqc_read_dups_plot.txt:md5,54f7e9aae54c41b712da0a1588e3140f", - "salmon.merged.gene_counts.tsv:md5,c14cab7e15cfac73ec0602dc2c404551", - "salmon.merged.gene_counts.tsv:md5,4d2f27b55f53ab117c936567d3cdb4db", - "salmon.merged.gene_counts_length_scaled.tsv:md5,71dbf161663fb316ce3a0092121ff31e", - "salmon.merged.gene_counts_length_scaled.tsv:md5,b24be2c7ef3bb2a35da5f4a39d4da781", - "salmon.merged.gene_counts_scaled.tsv:md5,15ee4df0aea058841e1862b2930ecd47", - "salmon.merged.gene_counts_scaled.tsv:md5,a2ce81d45d754640b13def3680162ed3", - "salmon.merged.gene_lengths.tsv:md5,558787c43000e5c4a8938a37966ad1ec", - "salmon.merged.gene_lengths.tsv:md5,b530c9b88a2d7b36df4e769cbcf37264", - "salmon.merged.gene_tpm.tsv:md5,ce8dfc4a096395e059459d24426cacf7", - "salmon.merged.gene_tpm.tsv:md5,16560ccf337a9852d590aaf932025da7", - "salmon.merged.transcript_counts.tsv:md5,ff0f5be09ca7a322672c0074ba35da17", - "salmon.merged.transcript_counts.tsv:md5,f2fb00a971c2766de62c48ae4db35bd5", - "salmon.merged.transcript_lengths.tsv:md5,f515488ac084048b3b7203b7fd6c1480", - "salmon.merged.transcript_lengths.tsv:md5,47b4184b99924dfdf06d86e6c3a53a65", - "salmon.merged.transcript_tpm.tsv:md5,e482a88dc193b80d14842ba901e85923", - "salmon.merged.transcript_tpm.tsv:md5,f61c786ea14038fbafd8eeffc37471a2", - "salmon_plot.txt:md5,6887931376c2dc556e8a1af3633ee432", - "samtools-flagstat-dp_Percentage_of_total.txt:md5,4854c1a00ee0f12c70faab85688ab3ae", - "samtools-flagstat-dp_Read_counts.txt:md5,9225d44fab730865089893c3013fa6ff", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", - "samtools-stats-dp.txt:md5,b803784736c9eaf7c28f882071144ad7", - "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", - "star_alignment_plot.txt:md5,77fc30308bc1b75bcf6e99630fc15344", - "star_summary_table.txt:md5,188cd28a8f309eb7c095694d79920eda", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] @@ -1271,7 +1139,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T11:35:18.063929" + "timestamp": "2024-09-13T18:15:12.604304" }, "Params: --min_mapped_reads 90 - stub": { "content": [ @@ -1355,20 +1223,13 @@ "trimgalore" ], [ - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T11:36:05.962174" + "timestamp": "2024-09-13T18:18:55.991093" } } \ No newline at end of file diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index ab3b51ac9..940a95bf9 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -1225,88 +1225,36 @@ "xls" ], [ - "RAP1_IAA_30M_REP1.bam_stat.txt:md5,4256d7f43715daff481bf0010b695981", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,f36792d25b268b6d556f8728300f4afc", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.txt:md5,c5865ded7168476d93057d2aedaec694", - "RAP1_IAA_30M_REP1.gene.abundance.txt:md5,ed17dbaed1006404f66247bd27b0daec", "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,ee69422d6e76fba223aa6b20a13027d2", - "RAP1_IAA_30M_REP1.inner_distance.txt:md5,b7a7d6298f58532d35941872f9edf1b3", - "RAP1_IAA_30M_REP1.inner_distance_freq.txt:md5,6d93d4f941ad8f61b35df2a0283caa66", - "RAP1_IAA_30M_REP1.inner_distance_mean.txt:md5,816bbb1a299cbfc822cf6377b7b77fda", - "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt:md5,e1480253d0cd3a0255b450737cc8fb58", - "RAP1_IAA_30M_REP1.read_distribution.txt:md5,37fadf8a5d3e6d4276fdcc217a0df8ab", - "RAP1_IAA_30M_REP1.stats.txt:md5,a87292c6f7166096166a9015c2e63dac", - "RAP1_IAA_30M_REP1.txt:md5,070ac8e0dd225793901887863446798d", - "RAP1_IAA_30M_REP1.txt:md5,c9edfeadc7fb5111837101a81af1c87e", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,ddadea4a08511aae6faeb632eb6aafea", "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,b21a53b0156b0afdfc28c237cb11218d", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,82764535b2fb80912383e5755d047fb6", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,ad270b5034d93ead92d24f8eaf8a8834", - "RAP1_UNINDUCED_REP1.bam_stat.txt:md5,d04cb03c42168319cb306f0b866b6b59", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,782f5001d411ba79314ba77f7d36b157", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,a0fb30c2b937a5a41ac865ab09367af7", - "RAP1_UNINDUCED_REP1.gene.abundance.txt:md5,4db684faae7a81432cd4020d434f6905", "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,ec9ec42ddfd3ffbb5373d3d6b6713b2c", - "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt:md5,66e3f455debd2224e43e2cac500a5dc5", - "RAP1_UNINDUCED_REP1.read_distribution.txt:md5,ac45c5dfa40382fd2613c85754dde373", - "RAP1_UNINDUCED_REP1.stats.txt:md5,781e49024150a8313779c574b58ad035", - "RAP1_UNINDUCED_REP1.txt:md5,49927ec2c47a93d48a3bbc62f6289c14", - "RAP1_UNINDUCED_REP1.txt:md5,18a36718e888c138c65f2a6ecd8862a7", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,1db4c86723cf69052c4386760a9750bb", "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,eccc5ca37855c717d35477e684188695", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,936795aee1462b84bcb2a6432a36f384", - "RAP1_UNINDUCED_REP2.bam_stat.txt:md5,5e114cb96f02f9fadd21e2a9826a68a6", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,1c9d07d9f9d12219d2b9f761f854eced", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,de016e691f5d56b13bbaa626ce2cc93e", - "RAP1_UNINDUCED_REP2.gene.abundance.txt:md5,7f5b66626bf039ca96290e2e73e9a8a8", "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,484e2860c6c496b1da5fac475a0cd3e4", - "RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt:md5,7381ffca14bddc77bb204b05c049f6e9", - "RAP1_UNINDUCED_REP2.read_distribution.txt:md5,de16f30d41f987f875e880bd3356d3f0", - "RAP1_UNINDUCED_REP2.stats.txt:md5,e455d0163bf2d988224b0c0092605213", - "RAP1_UNINDUCED_REP2.txt:md5,a9278cb2b25db32f9f6af60ca8789ca8", - "RAP1_UNINDUCED_REP2.txt:md5,6bd573fd119f84464dfca6044fe41704", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,c0bf1135d2d70c5918d87f706c0c54bc", "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,c3900f3bb24cd339d0e0ecf65ae43217", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,3ba3d5fbbf70d30eaf1632345e3d43a9", - "WT_REP1.bam_stat.txt:md5,bc6521a8455de55571a3ae6ef5a07aa2", "WT_REP1.biotype_counts_mqc.tsv:md5,eca4a76b9243248d01df5f4289b8201e", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", "WT_REP1.featureCounts.txt:md5,7aadafd0a26f5047a9ae7266eccfce05", - "WT_REP1.gene.abundance.txt:md5,904f2a58cb2af548cca532106096f6a9", "WT_REP1.infer_experiment.txt:md5,298c430c61cb7a46b48af867a0dfe00b", - "WT_REP1.inner_distance.txt:md5,053865cdb36070a6dc8bcb2d8214b037", - "WT_REP1.inner_distance_freq.txt:md5,8617bb6cc0009d8df2b52de14723d12e", - "WT_REP1.inner_distance_mean.txt:md5,1b39c2bb18142dc81882eeb60f677088", - "WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt:md5,73d281fa42d354a76e6a10e57f6ec451", - "WT_REP1.read_distribution.txt:md5,b72fac25d0cf554a657029290ca20bdd", - "WT_REP1.stats.txt:md5,6eab6936804c1157d5e1c61c0562d7de", - "WT_REP1.txt:md5,ec8f0bdfaa7bb558c91e0db2679eec8f", - "WT_REP1.txt:md5,118f0ab1b07ae7f4ef0b0bbdf738770d", "WT_REP1_dupMatrix.txt:md5,b0de1683f2a9bfa42437e924a11648fd", "WT_REP1_intercept_slope.txt:md5,f38c8525b7fcb990b7158f1518e451ad", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,a95807adf9df96f86a2f3fe3f244aebc", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,f7e6322095ed52defa0cbc931f935a75", - "WT_REP2.bam_stat.txt:md5,22fd302c0f8ab19b114caa4b8d47a92c", "WT_REP2.biotype_counts_mqc.tsv:md5,530605b80da27915a90d452249f3243a", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", "WT_REP2.featureCounts.txt:md5,809af01851125c401d576c21efca7b5a", - 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"ambig_info.tsv:md5,54d942ddf69b4e8f1598064e09428256", "ambig_info.tsv:md5,00a1f9de7095a68dfb43e0a0301b6ecd", "ambig_info.tsv:md5,933feffdaf6cf6ff407469ade0d7684d", @@ -1345,10 +1293,6 @@ "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", - "deseq2.pca.vals.txt:md5,37933c89d1b1b9755bece5ecd78bf260", - "deseq2.pca.vals.txt:md5,5f1a8fbbf3eb415ba5fe737419cdd6da", - "deseq2.sample.dists.txt:md5,12a45ba43afc5a42b207f4365382352b", - "deseq2.sample.dists.txt:md5,e34d3ebd6894757ba51da58ed7b546bb", "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", @@ -1369,121 +1313,29 @@ 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"meta_info.json:md5,885a6f8b06ae4ad2e30d600d8536cdc8", "multiqc_citations.txt:md5,bfa9fd61367cd7265e324d009c974778", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_dupradar-section-plot.txt:md5,dee44a480e3af641f1c377e0fb51d581", - "multiqc_fail_strand_check_table.txt:md5,0ccfa868ffd63cc403cf479161644563", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,54f0eef4ab0ecf6a03505b18752b43cd", - "multiqc_general_stats.txt:md5,fbca5b6c3cdb59f6c324014bfbdd1f87", - "multiqc_picard_dups.txt:md5,5e93e7e4ecaeed2550bffa44dc32184b", - "multiqc_rseqc_bam_stat.txt:md5,e4408b581842f3458e1b4efcdd178bc0", - "multiqc_rseqc_infer_experiment.txt:md5,e75efa2a05a2bbdf2d7f0bca788d9f81", - "multiqc_rseqc_junction_annotation.txt:md5,e67493668e9b93f6e15c145d8d844372", - "multiqc_rseqc_read_distribution.txt:md5,0132183561c399a5b57eee5f82bda19e", - "multiqc_salmon.txt:md5,64c8204709e83d24d75305170a173396", - "multiqc_salmon_deseq2_clustering-plot.txt:md5,01617c3802b9dcfbb0315acc70d122dc", - "multiqc_salmon_deseq2_clustering-plot_1.txt:md5,a2f09da18c91024118618580eb3789bd", - "multiqc_salmon_deseq2_clustering-plot_2.txt:md5,17552af947b4535158012647646918fe", - "multiqc_salmon_deseq2_clustering-plot_3.txt:md5,1841b06325df46fb8424a2d6b4f12746", - "multiqc_salmon_deseq2_clustering-plot_4.txt:md5,9f017597b413084aa2f8c57afeaeba2e", - "multiqc_salmon_deseq2_pca-plot.txt:md5,c7ecc952473b5755df30aaba0b53f3e6", - "multiqc_samtools_flagstat.txt:md5,cf062e6fc8eec3cbd81af8f3a1760fb8", "multiqc_samtools_idxstats.txt:md5,413ba06f3d8e4ab0dbde8ef8952c4b32", - "multiqc_samtools_stats.txt:md5,e810aae660c4255a9a6052825c554190", "multiqc_sortmerna.txt:md5,6eda2b8f75acaf145bd12ce3a5aff0e3", - "multiqc_star.txt:md5,3d7971209ef2c4c6784c6c349ceb5806", - "multiqc_star_salmon_deseq2_clustering-plot.txt:md5,99d097781c6761b6894e6bcc7999e1ba", - "multiqc_star_salmon_deseq2_clustering-plot_1.txt:md5,88bcc02233b2df2876678d186df8d32a", - "multiqc_star_salmon_deseq2_clustering-plot_2.txt:md5,8673d08e63e16dc7993f99f15c8377e1", - "multiqc_star_salmon_deseq2_clustering-plot_3.txt:md5,b65a05ab4904d2992d3bf664ad0e82f1", - "multiqc_star_salmon_deseq2_clustering-plot_4.txt:md5,5c77c5fefc953051de1fc1e6d8377cf2", - "multiqc_star_salmon_deseq2_pca-plot.txt:md5,da08bde54d271367ca718418508c10e9", - "picard_deduplication.txt:md5,32d912bd78e7d99276a52e13575d08aa", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,50e9209baeaafe181ce3b5caa05cf789", "qualimap_gene_coverage_profile_Normalised.txt:md5,6ed32f112c679e73396350cbe5cb9459", - "qualimap_genomic_origin.txt:md5,d0c0d1c67bfaa14dbdd7ded00ece8565", "qualimap_rnaseq_cov_hist.txt:md5,a895b3af229f661da1edbc21ec72edaa", - "qualimap_rnaseq_genome_results.txt:md5,b894c46e703a343da6d69ee55599c727", - "rnaseq_qc_results.txt:md5,84879fb36ed25857057d6c454a53b8f0", - "rnaseq_qc_results.txt:md5,ec01623528b9eb3e11547262f1f72ad9", - "rnaseq_qc_results.txt:md5,3f9f5d5acac942709d114bf3db75baa2", - "rnaseq_qc_results.txt:md5,7c902840996e1c660446122723e838e1", - "rnaseq_qc_results.txt:md5,d404a7d6838b9f3d4f6318acbc12cc69", - "rseqc_bam_stat.txt:md5,7a35d200db642e6b0ea269a8f934b345", "rseqc_infer_experiment_plot.txt:md5,d8741451248f1a5a4ebe3230c1af9c95", - "rseqc_inner_distance.txt:md5,260abe36852b01218e18446370e736d6", - "rseqc_inner_distance_plot_Counts.txt:md5,85405bfca2b42b4587814acd46d667ad", - "rseqc_inner_distance_plot_Percentages.txt:md5,f0d1f2edc65138cb659247fdcb66873f", - "rseqc_junction_annotation_junctions_plot_Events.txt:md5,1dfd3130b0f3a45541ef15fd2525d044", - "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,f4aa74934a4c73c2c8a1b78866090419", - "rseqc_junction_saturation_all.txt:md5,c8703dab7528a9a0ca1c502a496566e6", - "rseqc_junction_saturation_plot_All_Junctions.txt:md5,9f00706c76808ed45153abaf49805e7c", - "rseqc_junction_saturation_plot_Known_Junctions.txt:md5,2c9cc336da27198a7d12a8da517333f3", - "rseqc_junction_saturation_plot_Novel_Junctions.txt:md5,f9eec1a0481b9bafe8b893457dd13f59", - "rseqc_read_distribution_plot.txt:md5,c9a534adc9cf9c1856712c04490a6303", - "rseqc_read_dups.txt:md5,4c7a03a869ee271178643705d6fe6d46", - "rseqc_read_dups_plot.txt:md5,deac8cf2fb64d0a6a218522426f0d6e9", - "salmon.merged.gene_counts.tsv:md5,08091284e64aa757ecc2196e792d8ae9", - "salmon.merged.gene_counts.tsv:md5,0ac9ea2571d5d0c2dcab0760707272ed", - "salmon.merged.gene_counts_length_scaled.tsv:md5,2a240d1dedd20919a34f22d23ecd88e4", - "salmon.merged.gene_counts_length_scaled.tsv:md5,7bbb966d1020ecd47ac979a9b9d18158", - "salmon.merged.gene_counts_scaled.tsv:md5,51e72aba3ef4fc45f713966f85301de3", - "salmon.merged.gene_counts_scaled.tsv:md5,ec1ee30dc2610125f98385385eae5139", - "salmon.merged.gene_lengths.tsv:md5,0b4d5baa07c16c5044b742552a9459c8", - "salmon.merged.gene_lengths.tsv:md5,0b0b61df87da797ba987b84d6d4a3490", - "salmon.merged.gene_tpm.tsv:md5,ed09d766c7ebb7fe69cabcb10639f1f6", - "salmon.merged.gene_tpm.tsv:md5,c474a723b6275d83029d84fbe4b47aa9", - "salmon.merged.transcript_counts.tsv:md5,1d3901693acd506370ce9e4e96b4ad1f", - "salmon.merged.transcript_counts.tsv:md5,4ca583ec312bf36e176b7623e119d3f1", - "salmon.merged.transcript_lengths.tsv:md5,833e07c1adbcad1da2e2c89bfd4e04ba", - "salmon.merged.transcript_lengths.tsv:md5,4b5c294320b03a6c35fc2cb4eb05a012", - "salmon.merged.transcript_tpm.tsv:md5,2b172d59854ed34dfe7433dd8e862a6e", - "salmon.merged.transcript_tpm.tsv:md5,c01472102bc8f9c0ea9a29f29266d0b1", - "salmon_plot.txt:md5,39afeb0f51ac58c79935eaa9be13f0ef", - "samtools-flagstat-dp_Percentage_of_total.txt:md5,7e807b6919004a0460ded0823b1e3507", - "samtools-flagstat-dp_Read_counts.txt:md5,0d250bbb1e1a4690e4c5d3270ddb3a2a", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,53addd7b78d8ae224920ec9b97489d72", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,97fc7bde65a7efc5ab3af48ef0400c20", - "samtools-stats-dp.txt:md5,d0fbfb61041b38e3e084283b50952b00", - "samtools_alignment_plot.txt:md5,207e0c3f557679f37350577364b8956d", "sortmerna-detailed-plot.txt:md5,245e3f5575f2886943c833a4d26e5b8c", - "star_alignment_plot.txt:md5,6a5b205870c9ce814449101fa3222507", - "star_summary_table.txt:md5,d9a83bb733258d1e31922365ff0e9a7a", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] @@ -1492,7 +1344,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T11:48:42.540209" + "timestamp": "2024-09-13T18:31:45.951867" }, "Params: --remove_ribo_rna - stub": { "content": [ @@ -1579,20 +1431,13 @@ "trimgalore" ], [ - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T11:49:33.901393" + "timestamp": "2024-09-13T18:32:37.410482" } } \ No newline at end of file diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index ea459fcea..252dbebf8 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -272,19 +272,6 @@ "tx2gene.tsv" ], [ - "RAP1_IAA_30M_REP1.stats.txt:md5,a87292c6f7166096166a9015c2e63dac", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,b64efca5b1f31cee893f00a00e43baea", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,326657738d1f79eb9bc7735f44264b83", - "RAP1_UNINDUCED_REP1.stats.txt:md5,781e49024150a8313779c574b58ad035", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,8265d3f3a4084617b6e1e27c2a9ed46c", - "RAP1_UNINDUCED_REP2.stats.txt:md5,e455d0163bf2d988224b0c0092605213", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,ed85a0b7af3b2776c065a570d13eacff", - "WT_REP1.stats.txt:md5,6eab6936804c1157d5e1c61c0562d7de", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,e88d0f0c93cf9f8377af01ed161389fe", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,4f43f1258e593219abbed5f25a087978", - "WT_REP2.stats.txt:md5,002ddf6b828d34979652a40f05462843", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,12a83e73496de77bd9ac8042be365616", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,e73defcfa375bacacb3eede4b65b7b74", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", @@ -308,36 +295,14 @@ "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c", "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "fastqc_top_overrepresented_sequences_table.txt:md5,cf612406874da4e582eaeaa956f7eb66", - "flenDist.txt:md5,1a0b01789aabfb817e776e1c364fac85", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "flenDist.txt:md5,0aaae0a7f00b6f4037bc77e5f78b78d1", - "flenDist.txt:md5,7e3ef392373f4de7bba7eb77cf93590e", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", - "meta_info.json:md5,e9132375893ce91db6947538e64dd43c", - "meta_info.json:md5,5618fe266a5291cfef64e02f2de0547f", - "meta_info.json:md5,9bfa0dba837c6ebd4003603548d8f4d1", - "meta_info.json:md5,0d553bac54eda6f2a0e9ec847fae2bed", - "meta_info.json:md5,d03a4f847bb05b6d512b48903981d95d", "multiqc_citations.txt:md5,f789abe663d4b4214f0ddeb413a7f150", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "multiqc_general_stats.txt:md5,2c469bcca2d53528005d27eabc8abe09", - "multiqc_salmon.txt:md5,c321e69be50c717245a31a3a1c99face", - "salmon.merged.gene_counts.tsv:md5,c14cab7e15cfac73ec0602dc2c404551", - "salmon.merged.gene_counts_length_scaled.tsv:md5,60c648d6bee7364d956c94e7b722c388", - "salmon.merged.gene_counts_scaled.tsv:md5,7d28536335720847d2646c5565c2a2e8", - "salmon.merged.gene_lengths.tsv:md5,dc106a20fd3f322d3122c7e718ad33ba", - "salmon.merged.gene_tpm.tsv:md5,b6d982b0a0bedf3859bd0a950137c43e", - "salmon.merged.transcript_counts.tsv:md5,ff0f5be09ca7a322672c0074ba35da17", - "salmon.merged.transcript_lengths.tsv:md5,8d33a65a9c07bd59b1aab7d847be1e1a", - "salmon.merged.transcript_tpm.tsv:md5,40350df578e9c6b42a4fd67d4fb9905b", - "salmon_plot.txt:md5,afe2f326b018c7109a67f0cc86f23dc1", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], @@ -345,7 +310,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T11:52:59.260944" + "timestamp": "2024-09-13T18:36:11.677764" }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ @@ -409,20 +374,13 @@ "trimgalore" ], [ - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T11:53:47.849117" + "timestamp": "2024-09-13T18:37:06.985778" } } \ No newline at end of file diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index a721f8cc5..1cdb95e33 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -67,21 +67,14 @@ "trimgalore" ], [ - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T12:01:25.63497" + "timestamp": "2024-09-13T18:45:06.0114" }, "Params: --skip_qc": { "content": [ @@ -677,29 +670,6 @@ "tx2gene.tsv" ], [ - "RAP1_IAA_30M_REP1.gene.abundance.txt:md5,f9d863eb7c592dae0a150bb75e6dfb11", - "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt:md5,a1ac573f9bc57f81c543aefea59022a3", - "RAP1_IAA_30M_REP1.stats.txt:md5,a87292c6f7166096166a9015c2e63dac", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,42776aa5e9cab092eb073da4d4c7124c", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,8ec0bb4adca2e3fd289cfafa6b2be050", - "RAP1_UNINDUCED_REP1.gene.abundance.txt:md5,43d91c4bd7de0dce0bd4c55a107b15f3", - "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt:md5,75c2d4e783c0df560e277450409f7e9b", - "RAP1_UNINDUCED_REP1.stats.txt:md5,781e49024150a8313779c574b58ad035", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,e3bbccfb1f8c63f16effda08cfd45399", - "RAP1_UNINDUCED_REP2.gene.abundance.txt:md5,1b6cd8a16d7b12f4e0b2da9d008799a6", - "RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt:md5,a6e51fe99583ec5ed8cd7e6240951452", - "RAP1_UNINDUCED_REP2.stats.txt:md5,e455d0163bf2d988224b0c0092605213", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,8d0f5b732f20faccfd64cee80f17192a", - "WT_REP1.gene.abundance.txt:md5,1c65d6c9fdf938cffbe9cc7e041e5c97", - "WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt:md5,72fc24c190522e9f12485d05b6d86df7", - "WT_REP1.stats.txt:md5,6eab6936804c1157d5e1c61c0562d7de", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,c434ff325565d7bbb61170f690b9c47b", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,0bf084724dc0560725f6ed33a0ec1d73", - "WT_REP2.gene.abundance.txt:md5,b470d8d9e5b556bcd5605d5f1984178a", - "WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt:md5,9c9d912d313da779954796571504d70f", - "WT_REP2.stats.txt:md5,002ddf6b828d34979652a40f05462843", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,99445b63af1e1efe3502e90d68640379", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,ae6a54ab0c56aade4574d3abb70c9bda", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", @@ -733,72 +703,21 @@ "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c", "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "fastqc_top_overrepresented_sequences_table.txt:md5,cf612406874da4e582eaeaa956f7eb66", - "flenDist.txt:md5,5bdd51baaad54a5d910a90ca9cb5437f", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "flenDist.txt:md5,236a3e518282fecf9e815eb0dd22683b", - "flenDist.txt:md5,7cbd44fc12e7736a2f1f1e6deb3faa74", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "flenDist.txt:md5,425385dfa0e5e690ac1ccde48b93ecd0", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "flenDist.txt:md5,d60bba7dd4bf325bc9f4c4ec57819d03", - "flenDist.txt:md5,bcbf5f1f5358db90b8553fb186cf559d", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", - "meta_info.json:md5,fe0d73479c8aab74d0419ad488a73487", - "meta_info.json:md5,daa42f959b5416e410e1c9912fc76be9", - "meta_info.json:md5,ff4d73b85b1cee2e19cc0ad036818b11", - "meta_info.json:md5,ffd0ca80f23ad695b3ba169b50c3a93e", - "meta_info.json:md5,cac0375eedfcad7817df18e28bfa50ba", - "meta_info.json:md5,ee69de2f03f56c2e65db8e9ddbbba1c5", - "meta_info.json:md5,f1d661cb5aa332fb52938657ed7693fb", - "meta_info.json:md5,1685dbd949da167dce5024857551da82", - "meta_info.json:md5,d0da723a07af4adf5866e11ef0f0e0ed", - "meta_info.json:md5,5d9dfc7a5f06ad51bf77344d03f6ab2c", "multiqc_citations.txt:md5,ef51c78faebdd32bad296ba14406b41e", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "multiqc_general_stats.txt:md5,969a8f0aef8268da66150d723614dddd", - "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", - "multiqc_salmon.txt:md5,ee8f766c9af9f0d59e0391b3f6d71426", - "multiqc_samtools_flagstat.txt:md5,6cd62fbbb46370e90ff5410703f2891f", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "multiqc_samtools_stats.txt:md5,ae13ad7897ec9421a019c20c42f0ea71", - "multiqc_star.txt:md5,ae82337a5f847c86e8ffe14e04dfeaee", - "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "salmon.merged.gene_counts.tsv:md5,c14cab7e15cfac73ec0602dc2c404551", - "salmon.merged.gene_counts.tsv:md5,3ed7b1d514a12b2f431f7c72ae23dbe2", - "salmon.merged.gene_counts_length_scaled.tsv:md5,a3a07da2e891c40946b5f1ef2f6a27cf", - "salmon.merged.gene_counts_length_scaled.tsv:md5,481e23d26ea61c92458c28e07f3a1729", - "salmon.merged.gene_counts_scaled.tsv:md5,cd1b35911fd7be645c25d35196f50d3a", - "salmon.merged.gene_counts_scaled.tsv:md5,2eb656e29a548c404bb156ef2a94206d", - "salmon.merged.gene_lengths.tsv:md5,b40feaa838ffc98302527a59f9449784", - "salmon.merged.gene_lengths.tsv:md5,1b2eabc542ecf32844a84cb6bc790188", - "salmon.merged.gene_tpm.tsv:md5,76efd7f38e43a63be56697d403e47b22", - "salmon.merged.gene_tpm.tsv:md5,39027568743c7700f3fdcbd301889b18", - "salmon.merged.transcript_counts.tsv:md5,ff0f5be09ca7a322672c0074ba35da17", - "salmon.merged.transcript_counts.tsv:md5,12b3582c8f1dbd390d17dfbb324e08f2", - "salmon.merged.transcript_lengths.tsv:md5,9851a32c4e3ea0788510772bf377839e", - "salmon.merged.transcript_lengths.tsv:md5,62042bda6561146111ebc6456e9e984b", - "salmon.merged.transcript_tpm.tsv:md5,0c326a20ed5dd089367d85284719dce3", - "salmon.merged.transcript_tpm.tsv:md5,5dcfd83512b20e14769ff4c50c58a22f", - "salmon_plot.txt:md5,c1ee15b5ae91e69a6bd6170d7db57734", - "samtools-flagstat-dp_Percentage_of_total.txt:md5,f871d2c9eeb56efc70923843fe772353", - "samtools-flagstat-dp_Read_counts.txt:md5,11679c9decb6aabc056a2c05e4a56dec", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", - "samtools-stats-dp.txt:md5,b803784736c9eaf7c28f882071144ad7", - "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", - "star_alignment_plot.txt:md5,a44811c928719507cee0f98da7492fd1", - "star_summary_table.txt:md5,32aab6812d43f3c850b739eda99990f1", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] @@ -807,6 +726,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T12:00:26.616669" + "timestamp": "2024-09-13T18:44:17.772711" } } \ No newline at end of file diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index cbb165718..9a501ec7e 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -1111,78 +1111,34 @@ "xls" ], [ - "RAP1_IAA_30M_REP1.bam_stat.txt:md5,61b223c87d780480bd9a2e0562278762", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,27087a1c2e3cc2a0826818a04fe2647f", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.txt:md5,e8ec41e6e79f378e2f301e245a4f8e73", - "RAP1_IAA_30M_REP1.gene.abundance.txt:md5,616ab9268280dadeabcadb9cba9164c7", "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,e1de3aba230cf3d40f04d682dfe4e803", - "RAP1_IAA_30M_REP1.inner_distance.txt:md5,ef8ba8f829d2a6ec8abd54f11e84cafe", - "RAP1_IAA_30M_REP1.inner_distance_freq.txt:md5,5e86dae6ba1acee0f033ff881440a237", - "RAP1_IAA_30M_REP1.inner_distance_mean.txt:md5,0004eb9d5a4575ed42d895e108652641", - "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt:md5,8531d12d816e9b28e1c642f5e7323460", - "RAP1_IAA_30M_REP1.read_distribution.txt:md5,d2265f322b4239ee0e50a5b35937290a", - "RAP1_IAA_30M_REP1.stats.txt:md5,73f44a18148f208e2202d70e1db867d5", - "RAP1_IAA_30M_REP1.txt:md5,73d1f80aee2396bb3881784366c0124d", - "RAP1_IAA_30M_REP1.txt:md5,599ce85ad54348a8f4cc40ac16f329e7", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,fdeebc4f056cbb52fee53e82c2e0096f", "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,7962ee6ba989f9af6465aaf1101ba13b", - "RAP1_UNINDUCED_REP1.bam_stat.txt:md5,7d933b77abe7a59ef47b5671321076b8", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,2e1d531352e9ad5935308e588dbaffe7", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,3afe2b0bcf265526c247016c32482314", - "RAP1_UNINDUCED_REP1.gene.abundance.txt:md5,e6dd32586398931908c259c8ed1f11b3", "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,0bc268f09da1676522f8adda63509f14", - "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt:md5,68cf508d235542f790a55927d79bc995", - "RAP1_UNINDUCED_REP1.read_distribution.txt:md5,6b4338726b40a96a1aafec8804e63a07", - "RAP1_UNINDUCED_REP1.stats.txt:md5,7556dbe6062c94f91d25d474b88c8ed3", - "RAP1_UNINDUCED_REP1.txt:md5,662ee4ce4d6adb86ed7accdd20ce11c1", - "RAP1_UNINDUCED_REP1.txt:md5,f9cc64385ca2c33d585f88ce58970aac", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,aa94a148bdbebec4e82cd18a00316506", "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,6c69ccc819c14847eef319b7fa8ccb4f", - "RAP1_UNINDUCED_REP2.bam_stat.txt:md5,6e95c51796b5b4b18131d534cde8647b", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,6fedc1d11bc8d558f61c4c4a6060040f", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,6fed16d5ab57aa762891fde0c3720160", - "RAP1_UNINDUCED_REP2.gene.abundance.txt:md5,226a482129a51f334abc4e366b4e8b6e", "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,be4b322faffa736ab6ac39ff39c7aa9d", - "RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt:md5,65b201edd8fcbd49bcc00540fb7dbd9a", - "RAP1_UNINDUCED_REP2.read_distribution.txt:md5,bbfbd17329509ec89ca9a1b673b2476e", - "RAP1_UNINDUCED_REP2.stats.txt:md5,d920f45697802b25da9558e978bf2ea5", - "RAP1_UNINDUCED_REP2.txt:md5,b596c96d4a7a0aa48e9546fd7923dda7", - "RAP1_UNINDUCED_REP2.txt:md5,85f77a2925480efa09ba96f86fb81a50", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,bf065e266566c3fb96dc9319a3ed12cf", "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,147b051de3f1e5c75821176851d13612", - "WT_REP1.bam_stat.txt:md5,08ff5d55d751c523390130b79e85e8ce", "WT_REP1.biotype_counts_mqc.tsv:md5,ddcf909eacd91a49cc4fd3beed0b74f4", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", "WT_REP1.featureCounts.txt:md5,5155de67cf7537016c9ded607797f5c5", - "WT_REP1.gene.abundance.txt:md5,c6986771f3bbe0aba4374a45dfa22ff5", "WT_REP1.infer_experiment.txt:md5,7e8c79fa27780693523ad7acd8f109c4", - "WT_REP1.inner_distance.txt:md5,2aa7591c28cfeec9e0de20b8369d673a", - "WT_REP1.inner_distance_freq.txt:md5,d2bec12be2fbe40c99609865543c90a4", - "WT_REP1.inner_distance_mean.txt:md5,874a52bcd5c733b286b6393eeff6dd2e", - "WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt:md5,b6008877981664c8f922e3c49f88b722", - "WT_REP1.read_distribution.txt:md5,4b2b087bcb6e978aa7b39a86cb4f9e6d", - "WT_REP1.stats.txt:md5,85a04631ae7da2d29ebe413864e9218f", - "WT_REP1.txt:md5,c773c633ec68817258b5ade09fd19862", - "WT_REP1.txt:md5,59d1672c2535747556fd5a402199cca3", "WT_REP1_dupMatrix.txt:md5,04512c8be70c1898d0262935ed5ec5bd", "WT_REP1_intercept_slope.txt:md5,395cde13da1a90cf4378be2597c4f297", - "WT_REP2.bam_stat.txt:md5,7f5195602e20002ac974ff360b2e2b0e", "WT_REP2.biotype_counts_mqc.tsv:md5,d5d731cea7c5083a54069c1820101ba3", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", "WT_REP2.featureCounts.txt:md5,94d2ccd74ec4338ddc8ad7bdbf297826", - "WT_REP2.gene.abundance.txt:md5,55d84a6b0a66637b0552c8ead2616dc6", "WT_REP2.infer_experiment.txt:md5,c895dbd41b5a075ad4032e2732145b6a", - "WT_REP2.inner_distance.txt:md5,5e5ebf9347b1a5de7a64928e8ab9da87", - "WT_REP2.inner_distance_freq.txt:md5,00fa44998871648b608a26ae1c0ace94", - "WT_REP2.inner_distance_mean.txt:md5,f85ec5534b8b56b7924b2bd7c6a7209d", - "WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt:md5,bcebaf20684f9ab4a8873a7dc94c3a46", - "WT_REP2.read_distribution.txt:md5,df27f1be0e2f7452f13fd35d6fa5a694", - "WT_REP2.stats.txt:md5,09924c6d00da519be6e87e0f741574a8", - "WT_REP2.txt:md5,188c3279e64790d106b934631c73c8e7", - "WT_REP2.txt:md5,a80760aa72eb6beecafc95194e4e44c6", "WT_REP2_dupMatrix.txt:md5,5052efd01f5086d394499b9c4626deb1", "WT_REP2_intercept_slope.txt:md5,7ddae43baa3c4e499fbc319b95627c41", "ambig_info.tsv:md5,2f4c6a5953e41252a89851a9a7c36d9b", @@ -1220,10 +1176,6 @@ "coverage_profile_along_genes_(total).txt:md5,f53cfe3e30c560e3261818c2e6df3d5d", "coverage_profile_along_genes_(total).txt:md5,8a5255e6f9f142bbd22c636296f41d72", "coverage_profile_along_genes_(total).txt:md5,031046ef33de379e0463fddc0b924ecd", - "deseq2.pca.vals.txt:md5,98ca6732c6680f6658191474b8f56ce7", - "deseq2.pca.vals.txt:md5,cadbff9ec9fe399f9d508aef7eab4ebf", - "deseq2.sample.dists.txt:md5,755a11b6cd96ee2f08d77e43cec56df3", - "deseq2.sample.dists.txt:md5,a43cb911826b15c8672e00b889b677d2", "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", @@ -1234,116 +1186,25 @@ "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", - "fastqc_top_overrepresented_sequences_table.txt:md5,e379e3c9153047b8c71eda7148b39ecf", - "flenDist.txt:md5,381f5506929dc1d63b3bdf3b69730e82", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "flenDist.txt:md5,20e1e43dace7ef690dbb62cd896c9fd8", - "flenDist.txt:md5,25062d03132df75cb4dab2946c73085c", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "flenDist.txt:md5,31e6c262d5ad71fa7740b984a7b2d745", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "flenDist.txt:md5,3f15ff4253657117316116534901ba32", - "flenDist.txt:md5,c41a73ffb89e45df8010022db481cc28", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "junction_saturation_known.txt:md5,6931b0ef20697786bf16e838b43d02cb", - "junction_saturation_novel.txt:md5,043ae021d35067082b2ba9a87299afe6", "lib_format_counts.json:md5,03f0b70a4bb428fab96c29f04f895b6f", "lib_format_counts.json:md5,f7b7048fd2ac63fd792e71b85e4ed6d1", "lib_format_counts.json:md5,4bf135c93c37f90c493f761f2709a28b", "lib_format_counts.json:md5,406e1457f0f0506bd8e605a217477436", "lib_format_counts.json:md5,afd2a0ddf0fd0ec4f99be898608a59db", - "meta_info.json:md5,258ce336dc7123395b24e1d5f5a5b632", - "meta_info.json:md5,5ada3ab83d62339ec2e54ee91e1b5e7f", - "meta_info.json:md5,671de9b0a3b43b2e1722d932eb6f0c3a", - "meta_info.json:md5,4f7b491741e869883e31fda26d5c9678", - "meta_info.json:md5,9a96621c15a83886cd7a8133ad1ee9ac", - "meta_info.json:md5,702532921905a324a86b9cd45b94aa28", - "meta_info.json:md5,bb1ef8f662dea3ff2e8bb19a524e6341", - "meta_info.json:md5,3b4a941c96c5cac79fc60490af09a17b", - "meta_info.json:md5,3895245ce15dbe6447ed0c988fa3bf80", - "meta_info.json:md5,fbab04f9254ffba4e453ddc4b4573658", "multiqc_citations.txt:md5,1f80cefb6f0103d9a316c396a9441a90", - "multiqc_dupradar-section-plot.txt:md5,cad8c965d5c288f4f0b918ad1890ad9d", - "multiqc_fail_strand_check_table.txt:md5,ea1d58dbed0993de15f60613c1a0bfde", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_featurecounts_biotype_plot.txt:md5,567475905baa63091cfd0560fb297e10", - "multiqc_general_stats.txt:md5,cfa78ca943bd2bf9c3ad61d8fcd700b8", - "multiqc_picard_dups.txt:md5,825db93f9329a134414feff0a3ce601c", - "multiqc_rseqc_bam_stat.txt:md5,9efab740d8eb05854150f2bfa787edf3", - "multiqc_rseqc_infer_experiment.txt:md5,360985ec3233b3cb7dd0689b8ea304fe", - "multiqc_rseqc_junction_annotation.txt:md5,a5bc9a08fbb3451d83e70cded2e09d19", - "multiqc_rseqc_read_distribution.txt:md5,c0fec0553634b5ed819b0d9ebaae55a5", - "multiqc_salmon.txt:md5,db09a28e2b8debd662bf6dc28f7c5e72", - "multiqc_salmon_deseq2_clustering-plot.txt:md5,9006a6c3a88ec01450e0b31fd34bda3f", - "multiqc_salmon_deseq2_clustering-plot_1.txt:md5,b8e22fb22f1b1fbdf9a9e419e24c1fe4", - "multiqc_salmon_deseq2_clustering-plot_2.txt:md5,5100540611eb6b27e2dbf5f67421645c", - "multiqc_salmon_deseq2_clustering-plot_3.txt:md5,7438d8fdd6ed7f7edf008894384d5b26", - "multiqc_salmon_deseq2_clustering-plot_4.txt:md5,8c77bf56d901dda608f79713c8c72b3c", - "multiqc_salmon_deseq2_pca-plot.txt:md5,1ed0282378ecb1eece2eb59d2d3da4fa", - "multiqc_samtools_flagstat.txt:md5,d13fcab56c7527c929082e6ccb108094", "multiqc_samtools_idxstats.txt:md5,adf5f32fa1485ad0f4dacdfedc7b4bbc", - "multiqc_samtools_stats.txt:md5,828a6987f8d24e97d5007a56c83092df", - "multiqc_star.txt:md5,62fe73cc61dd4ff6eb5340f9d17924b1", - "multiqc_star_salmon_deseq2_clustering-plot.txt:md5,d1b71a3be04aaa74aeed57c876228400", - "multiqc_star_salmon_deseq2_clustering-plot_1.txt:md5,4061d0604e7663db5b0e3e26366c2491", - "multiqc_star_salmon_deseq2_clustering-plot_2.txt:md5,445cb200f2a77024f3b8da0676a7fbb1", - "multiqc_star_salmon_deseq2_clustering-plot_3.txt:md5,4185377be860ed8ba35c05ef095c074c", - "multiqc_star_salmon_deseq2_clustering-plot_4.txt:md5,be969cb3c9175f5f4f1e33d43543a13a", - "multiqc_star_salmon_deseq2_pca-plot.txt:md5,40c9a1a1fb3d228d3b3b92983e442850", - "picard_deduplication.txt:md5,b14cb08fecb135e93b8dd4e16f9e44fd", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,b16bc0437cb340aaf6fa1472888b6930", "qualimap_gene_coverage_profile_Normalised.txt:md5,209b0020fcd4c3c497e3abbd1f8cd593", - "qualimap_genomic_origin.txt:md5,2f6df8cec15cc1127b11990e928cf0f0", "qualimap_rnaseq_cov_hist.txt:md5,3be7bc41531ce84b42092a742bfeb0ab", - "qualimap_rnaseq_genome_results.txt:md5,0e038487a11ed226d6db717ae7bd5057", - "rnaseq_qc_results.txt:md5,64194a3c85869b302ccf725975b854ab", - "rnaseq_qc_results.txt:md5,c2d014351b3b4b412806fea4b6b04e93", - "rnaseq_qc_results.txt:md5,7333f74e4a3377e6cfe65eaf3a19ab62", - "rnaseq_qc_results.txt:md5,8f0abfb35f53c1f7618cc6f80482db23", - "rnaseq_qc_results.txt:md5,5b54f2f021022adcd00e4aaaed350524", - "rseqc_bam_stat.txt:md5,6b9f3a683f25d5cc8d386b42b928b085", "rseqc_infer_experiment_plot.txt:md5,382397ae264336395e2a3b03af8d7023", - "rseqc_inner_distance.txt:md5,ee47df0ab773f5b167b4a509e228825a", - "rseqc_inner_distance_plot_Counts.txt:md5,e7c620a381f0bd8b888e269dfd5f2e4a", - "rseqc_inner_distance_plot_Percentages.txt:md5,6aa0e5059fa706a043087fe2fbba6e3f", - "rseqc_junction_annotation_junctions_plot_Events.txt:md5,c97b783c5e1ac62d255c8df4d958985c", - "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,426b963c80ceb1ec4849d03da27e0570", - "rseqc_junction_saturation_all.txt:md5,c029cf0f56108652950a14bc7499e2eb", - "rseqc_junction_saturation_plot_All_Junctions.txt:md5,8093de8148484682ae7131691615f471", - "rseqc_junction_saturation_plot_Known_Junctions.txt:md5,6f26cac7325ab007f7428af12ef8d73d", - "rseqc_junction_saturation_plot_Novel_Junctions.txt:md5,07388858d309d0d1b8044b73b56d36f8", - "rseqc_read_distribution_plot.txt:md5,9ac572742f165b01d0f9f50f7671475a", - "rseqc_read_dups.txt:md5,812af3f856fdade8a775c4cefc9e26e0", - "rseqc_read_dups_plot.txt:md5,37b8146250793d2d2558d12607d64b51", - "salmon.merged.gene_counts.tsv:md5,559fb3c547c9446957d1cb126d038de8", - "salmon.merged.gene_counts.tsv:md5,5bde298638921461d4d2e311e7dc8d4b", - "salmon.merged.gene_counts_length_scaled.tsv:md5,1abd4ba39b1ecae6ed3a3fe4e2395d4c", - "salmon.merged.gene_counts_length_scaled.tsv:md5,4dd032f39327ee39fa3774a3f98cc27f", - "salmon.merged.gene_counts_scaled.tsv:md5,327fd44d5350de75c31a63ffc309de3b", - "salmon.merged.gene_counts_scaled.tsv:md5,0f97c726466b4eea1cf84a0a2db2d89e", - "salmon.merged.gene_lengths.tsv:md5,3cbc777e507b1b2b3f0eb76a7c61e52b", - "salmon.merged.gene_lengths.tsv:md5,8a072dae80a8a07a1191adea2b82030b", - "salmon.merged.gene_tpm.tsv:md5,7af4521545a5eac19f818b9cc507a1dd", - "salmon.merged.gene_tpm.tsv:md5,87c4cf0d14173580b38fa25c7130539e", - "salmon.merged.transcript_counts.tsv:md5,7745973ad4d62e71b788093edca1d7b3", - "salmon.merged.transcript_counts.tsv:md5,1182cfed65c7c45d083b26e18a17e13b", - "salmon.merged.transcript_lengths.tsv:md5,843866761ef13ffd76686dd2a48b71b7", - "salmon.merged.transcript_lengths.tsv:md5,28455afac83a9725fc12cbe39d2a1160", - "salmon.merged.transcript_tpm.tsv:md5,473035356f9bbbbb67a6a093f41cd8d8", - "salmon.merged.transcript_tpm.tsv:md5,43c014a9376bcbfc1d72c54a1ab8edad", - "salmon_plot.txt:md5,796493ded5a7223744d0a58197ef3b0f", - "samtools-flagstat-dp_Percentage_of_total.txt:md5,10e449fb6fc669f7fd9122b4f018bbe8", - "samtools-flagstat-dp_Read_counts.txt:md5,9743252bf8b1af3792018da22b65d1ac", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,a557130553131c893398532377d3b525", - "samtools-stats-dp.txt:md5,7895f53b9c164697c82daf5bfe55461f", - "samtools_alignment_plot.txt:md5,8a3a4dfbbfc068f150836ab6e163424a", - "star_alignment_plot.txt:md5,6858f5cc67b49ee908b4cf704b3762c8", - "star_summary_table.txt:md5,3bef1e0dd17e1bde7d0f24611127adca", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] @@ -1352,6 +1213,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T12:08:36.646809" + "timestamp": "2024-09-13T18:53:09.394964" } } \ No newline at end of file diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index aeb02255c..7149ad28d 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -1136,88 +1136,36 @@ "xls" ], [ - "RAP1_IAA_30M_REP1.bam_stat.txt:md5,bca6551fa4e1f59c46ffb8d02380260c", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,e66cd2b584d970ae3827ad2521f795ca", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.txt:md5,b3013c797d2fd38a8efa39047f5ba1b1", - "RAP1_IAA_30M_REP1.gene.abundance.txt:md5,c6cd1f4ab711bdd281708775a9047efc", "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,1f31ddae1f98e779e30d846cde3834de", - "RAP1_IAA_30M_REP1.inner_distance.txt:md5,415bc70baa08b22c47999a4c07dc30e2", - "RAP1_IAA_30M_REP1.inner_distance_freq.txt:md5,84b4e87f9a3af512253f1d6ee2be8659", - "RAP1_IAA_30M_REP1.inner_distance_mean.txt:md5,592b7ae36b515d70944f0e9a92af0913", - "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt:md5,4b7d5e90f795661a1bbe16e5a4441ac9", - "RAP1_IAA_30M_REP1.read_distribution.txt:md5,90de22c225fe5ecff10726adae623009", - "RAP1_IAA_30M_REP1.stats.txt:md5,a87292c6f7166096166a9015c2e63dac", - "RAP1_IAA_30M_REP1.txt:md5,070ac8e0dd225793901887863446798d", - "RAP1_IAA_30M_REP1.txt:md5,df79f656ddf47886895f8f786fb2b904", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,8da31020df3c5b25167345609c6d08c5", "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,d280fe126a5e82d24121d8662fd5a161", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,5ece339fc9945a4df104ca1297b47417", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,fa39381bd64f75a74fc02947985a552e", - "RAP1_UNINDUCED_REP1.bam_stat.txt:md5,1ef7ff325fb28e485ad2c6b64b0bd126", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,548023e639f8eb76f973a2f98bcbc82c", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,ff59317794fc04d5a4fd18797f0ecb0f", - "RAP1_UNINDUCED_REP1.gene.abundance.txt:md5,de3f0043b2c1b0309cf3c02027d31e2b", "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,a2a8e31dbd0ebd0c12f3f968ffd5391b", - "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt:md5,05263b9c173d4446601d7e6357279392", - "RAP1_UNINDUCED_REP1.read_distribution.txt:md5,d1248d1d29aad1a3b5ca799380f411e4", - "RAP1_UNINDUCED_REP1.stats.txt:md5,781e49024150a8313779c574b58ad035", - "RAP1_UNINDUCED_REP1.txt:md5,49927ec2c47a93d48a3bbc62f6289c14", - "RAP1_UNINDUCED_REP1.txt:md5,382c85d5970b54e389b678d9c21daf16", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,3f269a6b2e9c8eaab66582e31d208dfc", "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,a498640b0f9e710311ebc3eb67cedbd0", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,ebcd92288554810ad91755f7e9a63aa6", - "RAP1_UNINDUCED_REP2.bam_stat.txt:md5,b302c18e643aa10c293b04c0194b276c", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,2c0b5696582493f7a50259679982a6b3", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,6ee84531ba255791a11b487b6aea75ab", - "RAP1_UNINDUCED_REP2.gene.abundance.txt:md5,0e40ebb24737ab66f537e55e9fa9ea3f", "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,9ec058d3a4162fd1b4c6175e2106eef4", - "RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt:md5,3b9828dba74657a80b828dfa3ab68f67", - "RAP1_UNINDUCED_REP2.read_distribution.txt:md5,24a0a1c381db13692b837e85bec2a148", - "RAP1_UNINDUCED_REP2.stats.txt:md5,e455d0163bf2d988224b0c0092605213", - "RAP1_UNINDUCED_REP2.txt:md5,a9278cb2b25db32f9f6af60ca8789ca8", - "RAP1_UNINDUCED_REP2.txt:md5,69b33f5e18c3d9b7c9bebd18b258afcb", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,7d96d6ddf1d12d43837b105865aeaafa", "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,a1c5346e3bad40546c793b8914a22e7e", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,9c3ea7f49d4cb455116377445a7d80fb", - "WT_REP1.bam_stat.txt:md5,84eeac9b473e6ec3e15bb787545f170f", "WT_REP1.biotype_counts_mqc.tsv:md5,512645a8f736eee160c4465e1940f4a5", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", "WT_REP1.featureCounts.txt:md5,289cc95971a3ec550e018659279c1f59", - "WT_REP1.gene.abundance.txt:md5,4114734731f4e09e9ef3d41696c9dd54", "WT_REP1.infer_experiment.txt:md5,d55921c0084806cdf49b9bd8653c8e09", - "WT_REP1.inner_distance.txt:md5,b91483155e6b1862e8459d7f638d92d9", - "WT_REP1.inner_distance_freq.txt:md5,9a30bd9bef6e222b4a78fd4cdaaf615a", - "WT_REP1.inner_distance_mean.txt:md5,db7e4453ecf96ac7a74dec3f3f3ca003", - "WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt:md5,34f4f953d6981b30b6ab85a5112c7450", - "WT_REP1.read_distribution.txt:md5,8d086ee6973bc29e2c64cccbe9a318ad", - "WT_REP1.stats.txt:md5,6eab6936804c1157d5e1c61c0562d7de", - "WT_REP1.txt:md5,ec8f0bdfaa7bb558c91e0db2679eec8f", - "WT_REP1.txt:md5,c48cfed863a6db885195756a81d01acc", "WT_REP1_dupMatrix.txt:md5,802dd0de10d9118943869239f8659c78", "WT_REP1_intercept_slope.txt:md5,9c2e2b7890427e79c97e65827102d965", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,77bfb545d32f4ca472a034a2fcf76b23", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,439fd235319a95fbc8a98b873bc7d6dd", - "WT_REP2.bam_stat.txt:md5,3ef68247bece22b620fdf69d51182591", "WT_REP2.biotype_counts_mqc.tsv:md5,d4957c0197636b68d27fbd60d388bba1", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", "WT_REP2.featureCounts.txt:md5,152d2f26df56a88fe4b27c742d8f7447", - "WT_REP2.gene.abundance.txt:md5,2d23dd5c33e99beb7a8af529c936a0a1", "WT_REP2.infer_experiment.txt:md5,fe87600c55f433ba995fe18bed5cf5f1", - "WT_REP2.inner_distance.txt:md5,f7aaf10d3900dd8e990dcd0bf9b8d69c", - "WT_REP2.inner_distance_freq.txt:md5,dfbf0533ba67e2f201fd741de81c3057", - "WT_REP2.inner_distance_mean.txt:md5,97d20bd29262c3373fa396c354c2c9fc", - "WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt:md5,e1c458bce1ac3478923e2217e211204e", - "WT_REP2.read_distribution.txt:md5,6ffdd5dc3c3ba712d2a2dc413b82afdd", - "WT_REP2.stats.txt:md5,002ddf6b828d34979652a40f05462843", - "WT_REP2.txt:md5,3761cdcd554d5b696a42fd83f0f4cab7", - "WT_REP2.txt:md5,69e7c0ac02667cc1c63fa57aeb341c22", "WT_REP2_dupMatrix.txt:md5,e97a3c8d2e606d7d4b40cd33eb0b96c4", "WT_REP2_intercept_slope.txt:md5,db7a36459f2036de6657e74d2c98a47c", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,501ddea0b7d3317ed47d67a79904a8ef", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,f66c3afc99471c25b1fc8542edadbd10", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", @@ -1246,10 +1194,6 @@ "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", - "deseq2.pca.vals.txt:md5,27d34023c7d31086de1ba3197f33dd19", - "deseq2.pca.vals.txt:md5,c9761e5f9f2e2f65a8ae454c09a0d8a4", - "deseq2.sample.dists.txt:md5,aa500ce0a6060f5b53b8d60ac917cea3", - "deseq2.sample.dists.txt:md5,33100b62a67e01a9933a4fa0ae28d383", "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", @@ -1270,105 +1214,40 @@ "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "fastqc_top_overrepresented_sequences_table-1.txt:md5,0c4651cf1a1eb99028ca07378bf652a2", - "fastqc_top_overrepresented_sequences_table.txt:md5,a415f85e91e40b3e33495c8966b589e6", - "flenDist.txt:md5,8660769bb04cc03b484af6324c3e5532", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "flenDist.txt:md5,f716d2197e6e9718a439159dfc2a4e56", - "flenDist.txt:md5,3a1763134402a6b1447e6d5acc1ee9ad", - "flenDist.txt:md5,2de170bdc9f6fd237d286429b292bb28", - "junction_saturation_known.txt:md5,c4f8392730a877401d0222d233888615", - "junction_saturation_novel.txt:md5,a55c010d59c044e81232e08558e22444", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", - "meta_info.json:md5,7bb1cbcb8b1cd4078ac35521e7d5c7ce", - "meta_info.json:md5,1701b4aae305c6727134785f73ad7553", - "meta_info.json:md5,613394321a1c173af192ab2b2c3620d3", - "meta_info.json:md5,a8abf491d1ce4a37134554f400d7c589", - "meta_info.json:md5,1349e458ee65ea083d51f0825c0229fb", "multiqc_citations.txt:md5,5a68f7972ea275b21b12acdf43447dfb", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_dupradar-section-plot.txt:md5,f7e7bd50b7658627f8dffd8c05db2395", - "multiqc_fail_strand_check_table.txt:md5,6228c53a91a6fc21b847eb544af58959", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,27bb37d346e8f0960c882a3676e219e8", - "multiqc_general_stats.txt:md5,203d2625f86ce3cc2b56f554557c0b15", - "multiqc_picard_dups.txt:md5,1942ec1ae3f0b11b12dd52fdac925b32", - "multiqc_rsem.txt:md5,6485689490e140f2cf7812133fd04b88", - "multiqc_rseqc_bam_stat.txt:md5,e04211f87cac91e41585f60b131cd635", - "multiqc_rseqc_infer_experiment.txt:md5,8ed206b7c2f2f779d19a97861838cbbd", - "multiqc_rseqc_junction_annotation.txt:md5,64daa08c50145b278bd933e124139aa1", - "multiqc_rseqc_read_distribution.txt:md5,9b1524e10f936fd53383e17dc403e76f", - "multiqc_salmon.txt:md5,f09dabf3474d7e93d18849e25cb10531", - "multiqc_salmon_deseq2_clustering-plot.txt:md5,c39fd219828df33259e48aadcdd1997c", - "multiqc_salmon_deseq2_clustering-plot_1.txt:md5,6ccabfcdd11d36e140a7d6615c73ae85", - "multiqc_salmon_deseq2_clustering-plot_2.txt:md5,792ce8a58aefbbd10c0f182fcbc37c7a", - "multiqc_salmon_deseq2_clustering-plot_3.txt:md5,3080d13dee6e437084f27937296ede8a", - "multiqc_salmon_deseq2_clustering-plot_4.txt:md5,c750d2fa8d6dc8a2370335a71d2fa637", - "multiqc_salmon_deseq2_pca-plot.txt:md5,831426c001fe69be0e1ab2bfe32a234b", - "multiqc_samtools_flagstat.txt:md5,ef3dddc91fd64f36b20962c7f043d746", + "multiqc_rsem.txt:md5,426cfb38a96c0d7111336be3164171fb", "multiqc_samtools_idxstats.txt:md5,1cbc64fc9713831a6f45effc0cfe6a39", - "multiqc_samtools_stats.txt:md5,bdfee8392add57463b80b0d3eddec1fa", "multiqc_star_rsem_deseq2_clustering-plot.txt:md5,62bd581d9ea4cc3fb2dbddeb82238ed2", "multiqc_star_rsem_deseq2_clustering-plot_1.txt:md5,acd14c14552684ef5783a490de0bc704", "multiqc_star_rsem_deseq2_clustering-plot_2.txt:md5,a1e6de655a4e8ec1328afa53fa90322f", "multiqc_star_rsem_deseq2_clustering-plot_3.txt:md5,826ff3d14aa99c72c5a4280c0ffe21e3", "multiqc_star_rsem_deseq2_clustering-plot_4.txt:md5,47a6c91d653c82ed64e5be77f919f2c9", "multiqc_star_rsem_deseq2_pca-plot.txt:md5,7a428c83a9dec1f43ecd4fbbea664ece", - "picard_deduplication.txt:md5,aef521977daedc21bb07887a26da1de1", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,387c07f2a93e3d13048c4cd788d1fcc3", "qualimap_gene_coverage_profile_Normalised.txt:md5,35f0b71796622269bc51cf1e7a0650ab", - "qualimap_genomic_origin.txt:md5,bfb3b823cbfa6fcdc318e46c0675bda9", "qualimap_rnaseq_cov_hist.txt:md5,a620cb9d1878e86e10e87500e98122f1", - "qualimap_rnaseq_genome_results.txt:md5,665d15b3e428563147f1b0348c85dea2", - "rnaseq_qc_results.txt:md5,c6b372a9d5d698fbf75ddd184fe3d07a", - "rnaseq_qc_results.txt:md5,784dff32354c1c85a61e4a9fbef5c289", - "rnaseq_qc_results.txt:md5,77c1480d2516f81673a04c2d475cd089", - "rnaseq_qc_results.txt:md5,96b0f204fe424d427fa3310eeab6090f", - "rnaseq_qc_results.txt:md5,e5ed58b152457846935c49841c8eda2a", "rsem.merged.gene_counts.tsv:md5,47f272199f24af4473c959df2a9149dc", "rsem.merged.gene_tpm.tsv:md5,a197b2d131dea75a83f9c219c23fb7a0", "rsem.merged.transcript_counts.tsv:md5,ffc75fd409d75edf5209e8e1af8ec8fc", "rsem.merged.transcript_tpm.tsv:md5,b836618c69d111edf635ce7244ee85e5", - "rsem_assignment_plot.txt:md5,c2a1498bd3bd3d3a6f7d10a763523aa0", - "rsem_multimapping_rates.txt:md5,05878dd307fa1666dd4cc1888de6257a", - "rseqc_bam_stat.txt:md5,0853ff66eb375e1392c802d36274e371", + "rsem_assignment_plot.txt:md5,136b1ca144da9a1b304ff3471ff44390", + "rsem_multimapping_rates.txt:md5,5d91bb56472834622e81e7919f746250", "rseqc_infer_experiment_plot.txt:md5,c0ddf72b026cdc54ad03e75eaa636f7e", - "rseqc_inner_distance.txt:md5,da86b46fb8153d953be3869ef0c5cefe", - "rseqc_inner_distance_plot_Counts.txt:md5,993ac66c12c5a94f1d37585e6acc8816", - "rseqc_inner_distance_plot_Percentages.txt:md5,2c03ba90ae2aa298747b058182f19142", - "rseqc_junction_annotation_junctions_plot_Events.txt:md5,94752c1e9a14b1fadea71a04692b135a", - "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,5919e07739a4772e79aef1e39d64e7b8", - "rseqc_junction_saturation_all.txt:md5,1dfec8462f9a6a290c011b491db27da4", - "rseqc_junction_saturation_plot_All_Junctions.txt:md5,742d7cecdaab3bf521979fdf7476fbba", - "rseqc_junction_saturation_plot_Known_Junctions.txt:md5,1be623d478cd5c178bd0321c6ec5e165", - "rseqc_junction_saturation_plot_Novel_Junctions.txt:md5,abe21211fd41a4295d86bb75651df197", - "rseqc_read_distribution_plot.txt:md5,f6663d2117da6db3f81f81dee1c51545", - "rseqc_read_dups.txt:md5,2e167ae7d48d4e38290bcfe562db7636", - "rseqc_read_dups_plot.txt:md5,3c31ba1ad0b77309bf2458678687e01f", - "salmon.merged.gene_counts.tsv:md5,c14cab7e15cfac73ec0602dc2c404551", - "salmon.merged.gene_counts_length_scaled.tsv:md5,a23d84352ba03134d22850a004a57a09", - "salmon.merged.gene_counts_scaled.tsv:md5,04ff91967ed0a8eb6e94fb17f017ab39", - "salmon.merged.gene_lengths.tsv:md5,4435087195843065a538a6678afc9e17", - "salmon.merged.gene_tpm.tsv:md5,c58623d93411f20d07df1be51225ec2a", - "salmon.merged.transcript_counts.tsv:md5,ff0f5be09ca7a322672c0074ba35da17", - "salmon.merged.transcript_lengths.tsv:md5,e6879d46c319e1d78f75f7a88dfa15e1", - "salmon.merged.transcript_tpm.tsv:md5,99a7a71fb080d3b531ecca25f79227ec", - "salmon_plot.txt:md5,077ac8fab72e615c51b36de5e90969d7", - "samtools-flagstat-dp_Percentage_of_total.txt:md5,4f5c646dd02f5bcf98e3b3c89e75dcab", - "samtools-flagstat-dp_Read_counts.txt:md5,3a53b9adbd79a8ab738d762ef862ac49", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3e67e07b5c978fa363965e8e90356eef", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,a83e44c5a22e014d377c41419175784c", - "samtools-stats-dp.txt:md5,90a7927f8029fa72e5c15d602e7a9cf3", - "samtools_alignment_plot.txt:md5,9d85dfce5f40f65d02bb38dbf80e8963", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], @@ -1376,7 +1255,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T12:15:26.141628" + "timestamp": "2024-09-13T19:00:15.428368" }, "Params: --aligner star_rsem - stub": { "content": [ @@ -1458,20 +1337,13 @@ "trimgalore" ], [ - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T12:16:18.731766" + "timestamp": "2024-09-13T19:01:09.265956" } } \ No newline at end of file From caa80e6d8acaaf9ca02d0e14cca60ae6c2366d6b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Sep 2024 21:08:50 +0200 Subject: [PATCH 040/100] update snapshots --- tests/default.nf.test.snap | 27 +------------------- tests/featurecounts_group_type.nf.test.snap | 27 +------------------- tests/hisat2.nf.test.snap | 17 +------------ tests/kallisto.nf.test.snap | 28 ++++++--------------- tests/lib/UTILS.groovy | 12 +++++++++ tests/min_mapped_reads.nf.test.snap | 27 +------------------- tests/remove_ribo_rna.nf.test.snap | 27 +------------------- tests/salmon.nf.test.snap | 17 +------------ tests/skip_qc.nf.test.snap | 27 +------------------- tests/skip_trimming.nf.test.snap | 27 +------------------- tests/star_rsem.nf.test.snap | 17 +------------ 11 files changed, 28 insertions(+), 225 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 1c445c8ca..bc151ed00 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1326,26 +1326,6 @@ "WT_REP2.infer_experiment.txt:md5,82e23b329ee60709f343bc2d17d43b14", "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5", "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e", - "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", - "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", - "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", - "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", - "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", - "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", - "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", - "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", - "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", - "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", "coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1", "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3", @@ -1384,11 +1364,6 @@ "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", - "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", - "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", - "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", - "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", @@ -1413,6 +1388,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T17:41:17.28886" + "timestamp": "2024-09-13T19:10:42.293397" } } \ No newline at end of file diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index ff0d10d42..eb282fb3d 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -1277,26 +1277,6 @@ "WT_REP2.infer_experiment.txt:md5,82e23b329ee60709f343bc2d17d43b14", "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5", "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e", - "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", - "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", - "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", - "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", - "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", - "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", - "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", - "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", - "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", - "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", "coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1", "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3", @@ -1335,11 +1315,6 @@ "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", - "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", - "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", - "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", - "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", @@ -1363,6 +1338,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T17:49:03.61297" + "timestamp": "2024-09-13T19:32:25.807531" } } \ No newline at end of file diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 69931c964..39ef8efd0 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -1198,16 +1198,6 @@ "WT_REP2.infer_experiment.txt:md5,230910b354a5531d1c4bf711ccd6e493", "WT_REP2_dupMatrix.txt:md5,5176c7447c4295f94e2683dd9995cea0", "WT_REP2_intercept_slope.txt:md5,38fbb93a419e666bc81020602852b1e2", - "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", - "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", - "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", - "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", - "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", "coverage_profile_along_genes_(high).txt:md5,be72a2c9023f6eb81bd5816af33abb65", "coverage_profile_along_genes_(high).txt:md5,a31cb4ba804080544072cd57fc1bdf1c", "coverage_profile_along_genes_(high).txt:md5,83d436e0ddb7435bb343db5e4dfb744a", @@ -1248,11 +1238,6 @@ "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "hisat2_pe_plot.txt:md5,ca416ae8b811b11fe4cad79ef583aa3e", "hisat2_se_plot.txt:md5,f8cd912353aa55e6e670b72a736b656c", - "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", - "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", - "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", - "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", - "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "multiqc_citations.txt:md5,da5043f8ab9b5bd51d91ccf3111c655e", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", @@ -1277,6 +1262,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T17:54:49.218047" + "timestamp": "2024-09-13T19:38:22.496001" } } \ No newline at end of file diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 524118315..038641021 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -226,11 +226,6 @@ "tx2gene.tsv" ], [ - "abundance.tsv:md5,a208e4943f6efb704f68463df3147a49", - "abundance.tsv:md5,6fd77021287360f5005c90807233ab23", - "abundance.tsv:md5,602da7c00d92c1f21905d1a316c4286b", - "abundance.tsv:md5,b6ae4ef44f718a789f58dc6451b6eebb", - "abundance.tsv:md5,a2c6108c384662f4da8c7b7fe8f27e02", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -244,24 +239,15 @@ "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c", "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "kallisto.merged.gene_counts.tsv:md5,8813a72fee7acc6683681adcd9c3205d", - "kallisto.merged.gene_counts_length_scaled.tsv:md5,385855f0371d9b09f5929943d0bd3c5c", - "kallisto.merged.gene_counts_scaled.tsv:md5,384a713001db2273d4aa6a0b5a365f88", - "kallisto.merged.gene_lengths.tsv:md5,360be233f67438b3c74b30d4ffb82217", - "kallisto.merged.gene_tpm.tsv:md5,1c757b30cf764af3021536ed58929b47", - "kallisto.merged.transcript_counts.tsv:md5,12b42da001ba7217d84158bfc1dafb93", - "kallisto.merged.transcript_lengths.tsv:md5,efb283191ff876ea179db50bfd67e1e8", - "kallisto.merged.transcript_tpm.tsv:md5,f4b96383c1270f734ff291e6cddfcb72", - "kallisto_alignment.txt:md5,fafc53710b8d3cd6d3e456a1bd8c30e0", + "kallisto_alignment.txt:md5,6f1850f735edb8c199ef69a2aeca746c", "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "multiqc_kallisto.txt:md5,6fae2082e277bdea611a80f98e124165", - "run_info.json:md5,309ff0ae944127e8b6791e76ac196a01", - "run_info.json:md5,ccf4a5962415c6f1adb6e7ae05c4b86c", - "run_info.json:md5,8d2d93f6a5c27b11d3e428f628385bb7", - "run_info.json:md5,d12554278f74e04f7e6614a8f6f0f3dd", - "run_info.json:md5,019d3f1b7684c2e153be759cbc388b8b", + "run_info.json:md5,8c5c575c26f57ba7a8401b428d2634d7", + "run_info.json:md5,b85d5d5838fa6f166806415ee9372ce2", + "run_info.json:md5,02d4007f4d08f4e63c837cb2eed0c729", + "run_info.json:md5,8e274a8414bae6b1b6fa8ab94889e657", + "run_info.json:md5,b89650dcbafac69a8bbc2001d1a4d8b7", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], @@ -269,7 +255,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T18:00:22.935935" + "timestamp": "2024-09-13T19:42:11.719429" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index c3910ca17..2d5db9b7a 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -30,6 +30,7 @@ class UTILS { // Stable files, but order is changing /ambig_info\.tsv/, + /abundance\.tsv/, /cmd_info\.json/, /coverage_profile_along_genes_(high)\.txt/, /coverage_profile_along_genes_(low)\.txt/, @@ -128,6 +129,7 @@ class UTILS { /multiqc_dupradar-section-plot\.txt/, /multiqc_fail_strand_check_table\.txt/, /multiqc_general_stats\.txt/, + /multiqc_kallisto\.txt/, /multiqc_picard_dups\.txt/, /multiqc_report.html/, /multiqc_rseqc_bam_stat\.txt/, @@ -289,6 +291,16 @@ class UTILS { /deseq2\.sample\.dists\.txt/, /deseq2\.size_factors\.RData/, + // To exclude from kallisto + /kallisto\.merged\.gene_counts\.tsv/, + /kallisto\.merged\.gene_counts_length_scaled\.tsv/, + /kallisto\.merged\.gene_counts_scaled\.tsv/, + /kallisto\.merged\.gene_lengths\.tsv/, + /kallisto\.merged\.gene_tpm\.tsv/, + /kallisto\.merged\.transcript_counts\.tsv/, + /kallisto\.merged\.transcript_tpm\.tsv/, + /kallisto\.merged\.transcript_lengths\.tsv/, + // To exclude from salmon quant /fld\.gz/, /meta_info\.json/, diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 004091643..567304f6b 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -1057,26 +1057,6 @@ "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,7d5705880188f9beab1939e08d6b8f40", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043", - "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", - "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", - "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", - "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", - "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", - "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", - "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", - "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", - "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", - "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8", "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3", @@ -1109,11 +1089,6 @@ "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", - "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", - "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", - "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", - "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fail_mapped_samples_table.txt:md5,5dd9b06f326b1a55d78878343af89927", @@ -1139,7 +1114,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T18:15:12.604304" + "timestamp": "2024-09-13T19:49:23.338173" }, "Params: --min_mapped_reads 90 - stub": { "content": [ diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 940a95bf9..f5a5b1a31 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -1255,26 +1255,6 @@ "WT_REP2.infer_experiment.txt:md5,18758f433cf5c19bce599e5329da39a9", "WT_REP2_dupMatrix.txt:md5,bab18079153627205e5d907d8dfba677", "WT_REP2_intercept_slope.txt:md5,9bcbc18d0d331fe3c972538456ffd5b2", - "ambig_info.tsv:md5,54d942ddf69b4e8f1598064e09428256", - "ambig_info.tsv:md5,00a1f9de7095a68dfb43e0a0301b6ecd", - "ambig_info.tsv:md5,933feffdaf6cf6ff407469ade0d7684d", - "ambig_info.tsv:md5,25ced9693254994a7878241225baabb6", - "ambig_info.tsv:md5,c83b0f9ebe9b8dfc284595ec56d4f092", - "ambig_info.tsv:md5,070c7d50eab5ce0f211cdb06f9d7cc29", - "ambig_info.tsv:md5,1b69f9b651dfa6799e310004c1e3309f", - "ambig_info.tsv:md5,b8c61854b56a1c9a0fc8f158ea0c7599", - "ambig_info.tsv:md5,6cd02367152bb2dd59a6f1f70df2d7f8", - "ambig_info.tsv:md5,8611b6c03f6aa1a5f3dfceb0e65ad4ef", - "cmd_info.json:md5,5523405c02d30489d276e5d734cb54da", - "cmd_info.json:md5,c8c6208e1082ec150de56679b2b8cfe3", - "cmd_info.json:md5,998c89efb00fa5e63fd1d18c0602a019", - "cmd_info.json:md5,306609f606004616a89ec50dc59f22b0", - "cmd_info.json:md5,6b367a9cdd2837b88890209459acf45f", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", "coverage_profile_along_genes_(high).txt:md5,a349232d75f6c0adab6afcd9f6cbbafb", "coverage_profile_along_genes_(high).txt:md5,634f447f91db940d2148af74cf36febd", "coverage_profile_along_genes_(high).txt:md5,3f76529bd723d5320c86cc407fbb3294", @@ -1313,11 +1293,6 @@ "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "lib_format_counts.json:md5,43fc5463eada79e466d6ba9848739f06", - "lib_format_counts.json:md5,f56087bcbd494c7fa78200f65a2400e2", - "lib_format_counts.json:md5,e6e3d7746e9abee6a0e097ae0ee1781a", - "lib_format_counts.json:md5,b814fed52bd197a64544086dba0f127a", - "lib_format_counts.json:md5,3f4d67ace359562564dd336aa47a479c", "multiqc_citations.txt:md5,bfa9fd61367cd7265e324d009c974778", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", @@ -1344,7 +1319,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T18:31:45.951867" + "timestamp": "2024-09-13T20:00:52.090372" }, "Params: --remove_ribo_rna - stub": { "content": [ diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 252dbebf8..89342b2fc 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -272,16 +272,6 @@ "tx2gene.tsv" ], [ - "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", - "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", - "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", - "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", - "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -295,11 +285,6 @@ "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c", "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", - "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", - "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", - "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", - "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "multiqc_citations.txt:md5,f789abe663d4b4214f0ddeb413a7f150", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", @@ -310,7 +295,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T18:36:11.677764" + "timestamp": "2024-09-13T20:04:29.708154" }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 1cdb95e33..1d9778367 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -670,26 +670,6 @@ "tx2gene.tsv" ], [ - "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", - "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", - "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", - "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", - "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", - "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", - "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", - "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", - "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", - "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -703,11 +683,6 @@ "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c", "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", - "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", - "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", - "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", - "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "multiqc_citations.txt:md5,ef51c78faebdd32bad296ba14406b41e", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", @@ -726,6 +701,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T18:44:17.772711" + "timestamp": "2024-09-13T20:10:34.073257" } } \ No newline at end of file diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 9a501ec7e..873ea60a8 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -1141,26 +1141,6 @@ "WT_REP2.infer_experiment.txt:md5,c895dbd41b5a075ad4032e2732145b6a", "WT_REP2_dupMatrix.txt:md5,5052efd01f5086d394499b9c4626deb1", "WT_REP2_intercept_slope.txt:md5,7ddae43baa3c4e499fbc319b95627c41", - "ambig_info.tsv:md5,2f4c6a5953e41252a89851a9a7c36d9b", - "ambig_info.tsv:md5,6ed1b46c69917d6af3f093f9503bb962", - "ambig_info.tsv:md5,5fff63493bf3c223707ac90b9bb3a8f3", - "ambig_info.tsv:md5,e099a9ec06de792219139248712f7f40", - "ambig_info.tsv:md5,0e0895adb376929bec8e0dd0677bf7d8", - "ambig_info.tsv:md5,8d2b5ec0c441d9e078610480d179d116", - "ambig_info.tsv:md5,f2aed38ba5251664024392bc89ae3f01", - "ambig_info.tsv:md5,44dad5d05b3c0c2ccb5a19a3a80333b3", - "ambig_info.tsv:md5,d1d3bd2a5617220b29a9063cb29f0578", - "ambig_info.tsv:md5,452bbc83465339d2467663b061400b95", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", "coverage_profile_along_genes_(high).txt:md5,6afb5ffc9ddad52f69c518e32118ac61", "coverage_profile_along_genes_(high).txt:md5,2745780cc56258bbe587f9b6db03e9e4", "coverage_profile_along_genes_(high).txt:md5,f7c11dace9fc4f446fc29e5db7b3ee24", @@ -1186,11 +1166,6 @@ "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", - "lib_format_counts.json:md5,03f0b70a4bb428fab96c29f04f895b6f", - "lib_format_counts.json:md5,f7b7048fd2ac63fd792e71b85e4ed6d1", - "lib_format_counts.json:md5,4bf135c93c37f90c493f761f2709a28b", - "lib_format_counts.json:md5,406e1457f0f0506bd8e605a217477436", - "lib_format_counts.json:md5,afd2a0ddf0fd0ec4f99be898608a59db", "multiqc_citations.txt:md5,1f80cefb6f0103d9a316c396a9441a90", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_featurecounts_biotype_plot.txt:md5,567475905baa63091cfd0560fb297e10", @@ -1213,6 +1188,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T18:53:09.394964" + "timestamp": "2024-09-13T20:17:47.057332" } } \ No newline at end of file diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 7149ad28d..f5faa2a75 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -1166,16 +1166,6 @@ "WT_REP2.infer_experiment.txt:md5,fe87600c55f433ba995fe18bed5cf5f1", "WT_REP2_dupMatrix.txt:md5,e97a3c8d2e606d7d4b40cd33eb0b96c4", "WT_REP2_intercept_slope.txt:md5,db7a36459f2036de6657e74d2c98a47c", - "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", - "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", - "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", - "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", - "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", "coverage_profile_along_genes_(high).txt:md5,70c95fbc100f14911d2cc348bdff1587", "coverage_profile_along_genes_(high).txt:md5,cdb2c00c43121e3beccd7f670b34e05e", "coverage_profile_along_genes_(high).txt:md5,a73462b9ecbd1d2c45d7ca84b5f7925b", @@ -1214,11 +1204,6 @@ "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", - "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", - "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", - "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", - "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "multiqc_citations.txt:md5,5a68f7972ea275b21b12acdf43447dfb", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", @@ -1255,7 +1240,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T19:00:15.428368" + "timestamp": "2024-09-13T20:24:06.671066" }, "Params: --aligner star_rsem - stub": { "content": [ From 03b6501866e0c00fa75d389397b2ce057931ed13 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Sep 2024 23:05:46 +0200 Subject: [PATCH 041/100] update snapshots --- tests/default.nf.test.snap | 17 +---------------- tests/featurecounts_group_type.nf.test.snap | 17 +---------------- tests/hisat2.nf.test.snap | 21 +++------------------ tests/kallisto.nf.test.snap | 7 +------ tests/lib/UTILS.groovy | 12 +++++++----- tests/min_mapped_reads.nf.test.snap | 11 +---------- tests/remove_ribo_rna.nf.test.snap | 17 +---------------- tests/skip_trimming.nf.test.snap | 17 +---------------- tests/star_rsem.nf.test.snap | 20 +------------------- 9 files changed, 17 insertions(+), 122 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index bc151ed00..f99da4e15 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1326,21 +1326,6 @@ "WT_REP2.infer_experiment.txt:md5,82e23b329ee60709f343bc2d17d43b14", "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5", "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e", - "coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1", - "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", - "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3", - "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8", - "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3", - "coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211", - "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d", - "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b", - "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", - "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff", - "coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211", - "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d", - "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b", - "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", - "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -1388,6 +1373,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T19:10:42.293397" + "timestamp": "2024-09-13T21:40:50.513158" } } \ No newline at end of file diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index eb282fb3d..61c408139 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -1277,21 +1277,6 @@ "WT_REP2.infer_experiment.txt:md5,82e23b329ee60709f343bc2d17d43b14", "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5", "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e", - "coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1", - "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", - "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3", - "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8", - "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3", - "coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211", - "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d", - "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b", - "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", - "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff", - "coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211", - "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d", - "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b", - "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", - "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -1338,6 +1323,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T19:32:25.807531" + "timestamp": "2024-09-13T21:48:46.254482" } } \ No newline at end of file diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 39ef8efd0..bd0f72b82 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -1198,21 +1198,6 @@ "WT_REP2.infer_experiment.txt:md5,230910b354a5531d1c4bf711ccd6e493", "WT_REP2_dupMatrix.txt:md5,5176c7447c4295f94e2683dd9995cea0", "WT_REP2_intercept_slope.txt:md5,38fbb93a419e666bc81020602852b1e2", - "coverage_profile_along_genes_(high).txt:md5,be72a2c9023f6eb81bd5816af33abb65", - "coverage_profile_along_genes_(high).txt:md5,a31cb4ba804080544072cd57fc1bdf1c", - "coverage_profile_along_genes_(high).txt:md5,83d436e0ddb7435bb343db5e4dfb744a", - "coverage_profile_along_genes_(high).txt:md5,b56043c3546cac003461c57abad93536", - "coverage_profile_along_genes_(high).txt:md5,9ffadadb953cc9ea1b1c01ac92fcdf61", - "coverage_profile_along_genes_(low).txt:md5,9fce120533ff57f8bc2a2f44f1b6decb", - "coverage_profile_along_genes_(low).txt:md5,f744e295c3d034b1a86e1dde8bb18eff", - "coverage_profile_along_genes_(low).txt:md5,58021e91f3595a0d6dc74abc41690638", - "coverage_profile_along_genes_(low).txt:md5,1b55d86defcc541643137497c4c6bb06", - "coverage_profile_along_genes_(low).txt:md5,fb281c857a2c4e093b0d8e1f756abf81", - "coverage_profile_along_genes_(total).txt:md5,9fce120533ff57f8bc2a2f44f1b6decb", - "coverage_profile_along_genes_(total).txt:md5,f744e295c3d034b1a86e1dde8bb18eff", - "coverage_profile_along_genes_(total).txt:md5,58021e91f3595a0d6dc74abc41690638", - "coverage_profile_along_genes_(total).txt:md5,1b55d86defcc541643137497c4c6bb06", - "coverage_profile_along_genes_(total).txt:md5,fb281c857a2c4e093b0d8e1f756abf81", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -1236,14 +1221,14 @@ "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "hisat2_pe_plot.txt:md5,ca416ae8b811b11fe4cad79ef583aa3e", + "hisat2_pe_plot.txt:md5,790eea3061c7b76d3a377f00b67c2d33", "hisat2_se_plot.txt:md5,f8cd912353aa55e6e670b72a736b656c", "multiqc_citations.txt:md5,da5043f8ab9b5bd51d91ccf3111c655e", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,d35ad008181f0f7be84d5770d17a3a65", - "multiqc_hisat2.txt:md5,998b80a66a54cf87a571d95d9d6d5798", + "multiqc_hisat2.txt:md5,8883842d3bca98a0b6651fcd0b3b8cca", "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1262,6 +1247,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T19:38:22.496001" + "timestamp": "2024-09-13T21:54:32.213023" } } \ No newline at end of file diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 038641021..632bc8d9e 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -243,11 +243,6 @@ "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "run_info.json:md5,8c5c575c26f57ba7a8401b428d2634d7", - "run_info.json:md5,b85d5d5838fa6f166806415ee9372ce2", - "run_info.json:md5,02d4007f4d08f4e63c837cb2eed0c729", - "run_info.json:md5,8e274a8414bae6b1b6fa8ab94889e657", - "run_info.json:md5,b89650dcbafac69a8bbc2001d1a4d8b7", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], @@ -255,7 +250,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T19:42:11.719429" + "timestamp": "2024-09-13T21:58:11.868418" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index 2d5db9b7a..3e29214cb 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -32,9 +32,7 @@ class UTILS { /ambig_info\.tsv/, /abundance\.tsv/, /cmd_info\.json/, - /coverage_profile_along_genes_(high)\.txt/, - /coverage_profile_along_genes_(low)\.txt/, - /coverage_profile_along_genes_(total)\.txt/, + /coverage_profile_along_genes_.*\.txt/, /lib_format_counts\.json/, // To exlude bbsplit files @@ -131,7 +129,8 @@ class UTILS { /multiqc_general_stats\.txt/, /multiqc_kallisto\.txt/, /multiqc_picard_dups\.txt/, - /multiqc_report.html/, + /multiqc_report\.html/, + /multiqc_rsem\.txt/, /multiqc_rseqc_bam_stat\.txt/, /multiqc_rseqc_infer_experiment\.txt/, /multiqc_rseqc_junction_annotation\.txt/, @@ -167,6 +166,8 @@ class UTILS { /qualimap_genomic_origin-pct\.svg/, /qualimap_genomic_origin\.txt/, /qualimap_rnaseq_genome_results\.txt/, + /rsem_assignment_plot\.txt/, + /rsem_multimapping_rates\.txt/, /rseqc_bam_stat\.pdf/, /rseqc_bam_stat\.png/, /rseqc_bam_stat\.svg/, @@ -298,8 +299,9 @@ class UTILS { /kallisto\.merged\.gene_lengths\.tsv/, /kallisto\.merged\.gene_tpm\.tsv/, /kallisto\.merged\.transcript_counts\.tsv/, - /kallisto\.merged\.transcript_tpm\.tsv/, /kallisto\.merged\.transcript_lengths\.tsv/, + /kallisto\.merged\.transcript_tpm\.tsv/, + /run_info\.json/, // To exclude from salmon quant /fld\.gz/, diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 567304f6b..e85867f82 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -1057,15 +1057,6 @@ "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,7d5705880188f9beab1939e08d6b8f40", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043", - "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", - "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8", - "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3", - "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d", - "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", - "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff", - "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d", - "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", - "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -1114,7 +1105,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T19:49:23.338173" + "timestamp": "2024-09-13T22:05:25.922653" }, "Params: --min_mapped_reads 90 - stub": { "content": [ diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index f5a5b1a31..000abcf45 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -1255,21 +1255,6 @@ "WT_REP2.infer_experiment.txt:md5,18758f433cf5c19bce599e5329da39a9", "WT_REP2_dupMatrix.txt:md5,bab18079153627205e5d907d8dfba677", "WT_REP2_intercept_slope.txt:md5,9bcbc18d0d331fe3c972538456ffd5b2", - "coverage_profile_along_genes_(high).txt:md5,a349232d75f6c0adab6afcd9f6cbbafb", - "coverage_profile_along_genes_(high).txt:md5,634f447f91db940d2148af74cf36febd", - "coverage_profile_along_genes_(high).txt:md5,3f76529bd723d5320c86cc407fbb3294", - "coverage_profile_along_genes_(high).txt:md5,5aee6c959137a8c9bfbd0ddaa79dddba", - "coverage_profile_along_genes_(high).txt:md5,f5ac8f74fcad5d9ac72dbb6b65184bd0", - "coverage_profile_along_genes_(low).txt:md5,b2c696661e6c524b1641eb7267c70edc", - "coverage_profile_along_genes_(low).txt:md5,db2e0acbe9f07c68bcd7e08e036f02d3", - "coverage_profile_along_genes_(low).txt:md5,b9be191fdec82c78057e083d3adf20dd", - "coverage_profile_along_genes_(low).txt:md5,d2742410803e0de7cc606ef118010ea8", - "coverage_profile_along_genes_(low).txt:md5,d66da6e3f49b0870184fc881a162e785", - "coverage_profile_along_genes_(total).txt:md5,b2c696661e6c524b1641eb7267c70edc", - "coverage_profile_along_genes_(total).txt:md5,db2e0acbe9f07c68bcd7e08e036f02d3", - "coverage_profile_along_genes_(total).txt:md5,b9be191fdec82c78057e083d3adf20dd", - "coverage_profile_along_genes_(total).txt:md5,d2742410803e0de7cc606ef118010ea8", - "coverage_profile_along_genes_(total).txt:md5,d66da6e3f49b0870184fc881a162e785", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -1319,7 +1304,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T20:00:52.090372" + "timestamp": "2024-09-13T22:17:34.737268" }, "Params: --remove_ribo_rna - stub": { "content": [ diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 873ea60a8..6b633070a 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -1141,21 +1141,6 @@ "WT_REP2.infer_experiment.txt:md5,c895dbd41b5a075ad4032e2732145b6a", "WT_REP2_dupMatrix.txt:md5,5052efd01f5086d394499b9c4626deb1", "WT_REP2_intercept_slope.txt:md5,7ddae43baa3c4e499fbc319b95627c41", - "coverage_profile_along_genes_(high).txt:md5,6afb5ffc9ddad52f69c518e32118ac61", - "coverage_profile_along_genes_(high).txt:md5,2745780cc56258bbe587f9b6db03e9e4", - "coverage_profile_along_genes_(high).txt:md5,f7c11dace9fc4f446fc29e5db7b3ee24", - "coverage_profile_along_genes_(high).txt:md5,59a01cd5d9bc7b6096490d7f3d6d6877", - "coverage_profile_along_genes_(high).txt:md5,61683a2fcf35174fe72a648be63d45ac", - "coverage_profile_along_genes_(low).txt:md5,248345fdf0f8de2a8d7d329edd0a5c42", - "coverage_profile_along_genes_(low).txt:md5,85154785601b18118ae2e6a19d0a1c0a", - "coverage_profile_along_genes_(low).txt:md5,f53cfe3e30c560e3261818c2e6df3d5d", - "coverage_profile_along_genes_(low).txt:md5,8a5255e6f9f142bbd22c636296f41d72", - "coverage_profile_along_genes_(low).txt:md5,031046ef33de379e0463fddc0b924ecd", - "coverage_profile_along_genes_(total).txt:md5,248345fdf0f8de2a8d7d329edd0a5c42", - "coverage_profile_along_genes_(total).txt:md5,85154785601b18118ae2e6a19d0a1c0a", - "coverage_profile_along_genes_(total).txt:md5,f53cfe3e30c560e3261818c2e6df3d5d", - "coverage_profile_along_genes_(total).txt:md5,8a5255e6f9f142bbd22c636296f41d72", - "coverage_profile_along_genes_(total).txt:md5,031046ef33de379e0463fddc0b924ecd", "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", @@ -1188,6 +1173,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T20:17:47.057332" + "timestamp": "2024-09-13T22:35:39.034925" } } \ No newline at end of file diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index f5faa2a75..8606efd66 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -1166,21 +1166,6 @@ "WT_REP2.infer_experiment.txt:md5,fe87600c55f433ba995fe18bed5cf5f1", "WT_REP2_dupMatrix.txt:md5,e97a3c8d2e606d7d4b40cd33eb0b96c4", "WT_REP2_intercept_slope.txt:md5,db7a36459f2036de6657e74d2c98a47c", - "coverage_profile_along_genes_(high).txt:md5,70c95fbc100f14911d2cc348bdff1587", - "coverage_profile_along_genes_(high).txt:md5,cdb2c00c43121e3beccd7f670b34e05e", - "coverage_profile_along_genes_(high).txt:md5,a73462b9ecbd1d2c45d7ca84b5f7925b", - "coverage_profile_along_genes_(high).txt:md5,31ab137e75752225365bd3d89143dbd2", - "coverage_profile_along_genes_(high).txt:md5,93822686a53dd40d3ff426ddbfc9314e", - "coverage_profile_along_genes_(low).txt:md5,86e56ef794277bcf1e0d121a088b8581", - "coverage_profile_along_genes_(low).txt:md5,1a9405c8bd7c00f3be082bfebb90b6ed", - "coverage_profile_along_genes_(low).txt:md5,7adc228bc15e344abb7938ea4d35a846", - "coverage_profile_along_genes_(low).txt:md5,eaceda909bf652b8301fa0ed1bba9ae1", - "coverage_profile_along_genes_(low).txt:md5,bd8d58c757e4122caee4b4e8df2f4b00", - "coverage_profile_along_genes_(total).txt:md5,86e56ef794277bcf1e0d121a088b8581", - "coverage_profile_along_genes_(total).txt:md5,1a9405c8bd7c00f3be082bfebb90b6ed", - "coverage_profile_along_genes_(total).txt:md5,7adc228bc15e344abb7938ea4d35a846", - "coverage_profile_along_genes_(total).txt:md5,eaceda909bf652b8301fa0ed1bba9ae1", - "coverage_profile_along_genes_(total).txt:md5,bd8d58c757e4122caee4b4e8df2f4b00", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -1209,7 +1194,6 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,27bb37d346e8f0960c882a3676e219e8", - "multiqc_rsem.txt:md5,426cfb38a96c0d7111336be3164171fb", "multiqc_samtools_idxstats.txt:md5,1cbc64fc9713831a6f45effc0cfe6a39", "multiqc_star_rsem_deseq2_clustering-plot.txt:md5,62bd581d9ea4cc3fb2dbddeb82238ed2", "multiqc_star_rsem_deseq2_clustering-plot_1.txt:md5,acd14c14552684ef5783a490de0bc704", @@ -1227,8 +1211,6 @@ "rsem.merged.gene_tpm.tsv:md5,a197b2d131dea75a83f9c219c23fb7a0", "rsem.merged.transcript_counts.tsv:md5,ffc75fd409d75edf5209e8e1af8ec8fc", "rsem.merged.transcript_tpm.tsv:md5,b836618c69d111edf635ce7244ee85e5", - "rsem_assignment_plot.txt:md5,136b1ca144da9a1b304ff3471ff44390", - "rsem_multimapping_rates.txt:md5,5d91bb56472834622e81e7919f746250", "rseqc_infer_experiment_plot.txt:md5,c0ddf72b026cdc54ad03e75eaa636f7e", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3e67e07b5c978fa363965e8e90356eef", @@ -1240,7 +1222,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T20:24:06.671066" + "timestamp": "2024-09-13T22:42:21.244724" }, "Params: --aligner star_rsem - stub": { "content": [ From 4dc9fb8d11a823ea33f73acabe1aa497dc4eeeef Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Sat, 14 Sep 2024 09:37:59 +0200 Subject: [PATCH 042/100] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c000cf69a..0baacb67a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ Special thanks to the following for their contributions to the release: - [PR #1374](https://github.com/nf-core/rnaseq/pull/1374) - Bump pipeline version to 3.16.0dev - [PR #1379](https://github.com/nf-core/rnaseq/pull/1379) - Enhance pipeline level test snapshots +- [PR #1380](https://github.com/nf-core/rnaseq/pull/1380) - Fix issues with R modules changing sample names - [PR #1381](https://github.com/nf-core/rnaseq/pull/1381) - Update all modules following massive conda usage update in nf-core modules ## [[3.15.0](https://github.com/nf-core/rnaseq/releases/tag/3.15.0)] - 2024-09-04 From 2be93d81529d672830915cda3a0286db60e31675 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Sat, 14 Sep 2024 10:04:36 +0200 Subject: [PATCH 043/100] update snapshots --- tests/hisat2.nf.test.snap | 6 ++---- tests/kallisto.nf.test.snap | 5 ++--- tests/lib/UTILS.groovy | 5 +++++ tests/remove_ribo_rna.nf.test.snap | 6 ++---- 4 files changed, 11 insertions(+), 11 deletions(-) diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index bd0f72b82..d5ab92294 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -89,7 +89,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T17:55:33.048993" + "timestamp": "2024-09-14T09:48:43.13292" }, "Params: --aligner hisat2": { "content": [ @@ -1221,14 +1221,12 @@ "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "hisat2_pe_plot.txt:md5,790eea3061c7b76d3a377f00b67c2d33", "hisat2_se_plot.txt:md5,f8cd912353aa55e6e670b72a736b656c", "multiqc_citations.txt:md5,da5043f8ab9b5bd51d91ccf3111c655e", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,d35ad008181f0f7be84d5770d17a3a65", - "multiqc_hisat2.txt:md5,8883842d3bca98a0b6651fcd0b3b8cca", "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1247,6 +1245,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T21:54:32.213023" + "timestamp": "2024-09-14T09:47:53.335596" } } \ No newline at end of file diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 632bc8d9e..433228a85 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -239,7 +239,6 @@ "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c", "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "kallisto_alignment.txt:md5,6f1850f735edb8c199ef69a2aeca746c", "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", @@ -250,7 +249,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T21:58:11.868418" + "timestamp": "2024-09-14T09:51:53.986015" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ @@ -324,6 +323,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T18:04:31.974316" + "timestamp": "2024-09-14T09:52:28.974644" } } \ No newline at end of file diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index 3e29214cb..6f12ca61d 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -121,12 +121,15 @@ class UTILS { /general_stats_table\.pdf/, /general_stats_table\.png/, /general_stats_table\.svg/, + /hisat2_pe_plot\.txt/, /junction_saturation_known\.txt/, /junction_saturation_novel\.txt/, + /kallisto_alignment\.txt/, /multiqc_data\.json/, /multiqc_dupradar-section-plot\.txt/, /multiqc_fail_strand_check_table\.txt/, /multiqc_general_stats\.txt/, + /multiqc_hisat2\.txt/, /multiqc_kallisto\.txt/, /multiqc_picard_dups\.txt/, /multiqc_report\.html/, @@ -142,6 +145,7 @@ class UTILS { /multiqc_samtools_flagstat\.txt/, /multiqc_samtools_stats\.txt/, /multiqc_software_versions\.txt/, + /multiqc_sortmerna\.txt/, /multiqc_sources\.txt/, /multiqc_star\.txt/, /multiqc_star_salmon_deseq2_clustering-plot\.txt/, @@ -262,6 +266,7 @@ class UTILS { /samtools_alignment_plot-pct\.png/, /samtools_alignment_plot-pct\.svg/, /samtools_alignment_plot\.txt/, + /sortmerna-detailed-plot\.txt/, /star_alignment_plot-cnt\.pdf/, /star_alignment_plot-cnt\.png/, /star_alignment_plot-cnt\.svg/, diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 000abcf45..f2cda5f25 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -1284,7 +1284,6 @@ "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,54f0eef4ab0ecf6a03505b18752b43cd", "multiqc_samtools_idxstats.txt:md5,413ba06f3d8e4ab0dbde8ef8952c4b32", - "multiqc_sortmerna.txt:md5,6eda2b8f75acaf145bd12ce3a5aff0e3", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1295,7 +1294,6 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,53addd7b78d8ae224920ec9b97489d72", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,97fc7bde65a7efc5ab3af48ef0400c20", - "sortmerna-detailed-plot.txt:md5,245e3f5575f2886943c833a4d26e5b8c", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] @@ -1304,7 +1302,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T22:17:34.737268" + "timestamp": "2024-09-14T10:03:34.943643" }, "Params: --remove_ribo_rna - stub": { "content": [ @@ -1398,6 +1396,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T18:32:37.410482" + "timestamp": "2024-09-14T10:04:28.342005" } } \ No newline at end of file From 6904250f1e7b0e046ef982ccbfc9ee90adbf1506 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 17 Sep 2024 11:37:06 +0200 Subject: [PATCH 044/100] do not sort output --- tests/default.nf.test.snap | 2202 ++++++++++++++++++------------------ tests/lib/UTILS.groovy | 16 +- 2 files changed, 1125 insertions(+), 1093 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index f99da4e15..b246da867 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -46,39 +46,39 @@ } }, [ - "RAP1_IAA_30M_REP1_raw.html", - "RAP1_IAA_30M_REP1_raw.zip", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_raw.html", - "RAP1_UNINDUCED_REP1_raw.zip", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "fastqc", + "trim", + "raw", "RAP1_UNINDUCED_REP2_raw.html", "RAP1_UNINDUCED_REP2_raw.zip", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_raw.zip", + 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"fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", + "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "qualimap_gene_coverage_profile_Counts.txt:md5,02044ed1bf1eca19a8a87c9971cdc049", - "qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa", + "multiqc_featurecounts_biotype_plot.txt:md5,56be7f0813c3cbea0f68f61d9b355b71", + "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", + "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", "qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce", - "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", - "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", - "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", + "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", + "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c", + "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", + "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", + "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e", + "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T21:40:50.513158" + "timestamp": "2024-09-17T11:26:28.121956" } } \ No newline at end of file diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index 6f12ca61d..a0be2e956 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -13,12 +13,11 @@ class UTILS { boolean matchesInclusion = (includeRegexes == null || includeRegexes.any { regex -> file.name.toString() ==~ regex }) boolean matchesExclusion = (excludeRegexes == null || !excludeRegexes.any { regex -> file.name.toString() ==~ regex }) - // Conditionally add either full path or just the file name - if (matchesInclusion && matchesExclusion) { - output.add(file) - } + // Conditionally add either file path or just the file name + if (matchesInclusion && matchesExclusion) output.add(file) + } - return output.sort { it.name } + return output } // Static (global) exclusion regexes list @@ -28,13 +27,6 @@ class UTILS { // To exclude files with timestamps in the format YYYY-MM-DD_HH-MM-SS /\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}/, - // Stable files, but order is changing - /ambig_info\.tsv/, - /abundance\.tsv/, - /cmd_info\.json/, - /coverage_profile_along_genes_.*\.txt/, - /lib_format_counts\.json/, - // To exlude bbsplit files /.*\.stats\.txt/, From 96c415d34424dd57ecc9924c952b1f51ffa1602b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 17 Sep 2024 12:35:57 +0200 Subject: [PATCH 045/100] sort output by PATH --- tests/default.nf.test.snap | 2312 ++++++++++++++++++------------------ tests/lib/UTILS.groovy | 2 +- 2 files changed, 1157 insertions(+), 1157 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index b246da867..3c2319ca0 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -46,39 +46,39 @@ } }, [ + "custom", + "out", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", "fastqc", - "trim", "raw", - "RAP1_UNINDUCED_REP2_raw.html", - "RAP1_UNINDUCED_REP2_raw.zip", - "RAP1_IAA_30M_REP1_raw.zip", "RAP1_IAA_30M_REP1_raw.html", - "WT_REP2_raw.html", - "RAP1_UNINDUCED_REP1_raw.zip", + "RAP1_IAA_30M_REP1_raw.zip", "RAP1_UNINDUCED_REP1_raw.html", + "RAP1_UNINDUCED_REP1_raw.zip", + "RAP1_UNINDUCED_REP2_raw.html", + "RAP1_UNINDUCED_REP2_raw.zip", "WT_REP1_raw.html", - "WT_REP2_raw.zip", "WT_REP1_raw.zip", + "WT_REP2_raw.html", + "WT_REP2_raw.zip", + "trim", + "multiqc", + "star_salmon", + "multiqc_data", + "multiqc_plots", + "multiqc_report.html", + "pipeline_info", + "nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "custom", - "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", - "pipeline_info", - "nf_core_rnaseq_software_mqc_versions.yml", - "multiqc", - "star_salmon", - "multiqc_data", - "multiqc_report.html", - "multiqc_plots" + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ @@ -88,7 +88,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T11:16:13.678086" + "timestamp": "2024-09-17T12:25:22.192471" }, "Params: default": { "content": [ @@ -228,1191 +228,1191 @@ } }, [ - "salmon", - "WT_REP1", - "quant.sf", - "lib_format_counts.json", - "logs", - "salmon_quant.log", - "libParams", - "flenDist.txt", - "cmd_info.json", - "aux_info", - "fld.gz", - "observed_bias.gz", - "meta_info.json", - "expected_bias.gz", - "ambig_info.tsv", - "observed_bias_3p.gz", - "quant.genes.sf", - "salmon.merged.transcript_lengths.tsv", - "RAP1_UNINDUCED_REP2", 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"observed_bias_3p.gz", - "quant.genes.sf", - "tx2gene.tsv", + "bbsplit", + "RAP1_IAA_30M_REP1.stats.txt", + "RAP1_UNINDUCED_REP1.stats.txt", + "RAP1_UNINDUCED_REP2.stats.txt", + "WT_REP1.stats.txt", + "WT_REP2.stats.txt", + "custom", + "out", + "genome_gfp.fasta", + "genome_gfp.gtf", + "fastqc", + "raw", + "RAP1_IAA_30M_REP1_raw_1_fastqc.html", + "RAP1_IAA_30M_REP1_raw_1_fastqc.zip", + "RAP1_IAA_30M_REP1_raw_2_fastqc.html", + "RAP1_IAA_30M_REP1_raw_2_fastqc.zip", + "RAP1_UNINDUCED_REP1_raw_fastqc.html", + "RAP1_UNINDUCED_REP1_raw_fastqc.zip", + "RAP1_UNINDUCED_REP2_raw_fastqc.html", + "RAP1_UNINDUCED_REP2_raw_fastqc.zip", + "WT_REP1_raw_1_fastqc.html", + "WT_REP1_raw_1_fastqc.zip", + "WT_REP1_raw_2_fastqc.html", + "WT_REP1_raw_2_fastqc.zip", + "WT_REP2_raw_1_fastqc.html", + "WT_REP2_raw_1_fastqc.zip", + "WT_REP2_raw_2_fastqc.html", + "WT_REP2_raw_2_fastqc.zip", + "trim", + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "WT_REP1_trimmed_1_val_1_fastqc.html", + "WT_REP1_trimmed_1_val_1_fastqc.zip", + "WT_REP1_trimmed_2_val_2_fastqc.html", + "WT_REP1_trimmed_2_val_2_fastqc.zip", + "WT_REP2_trimmed_1_val_1_fastqc.html", + "WT_REP2_trimmed_1_val_1_fastqc.zip", + "WT_REP2_trimmed_2_val_2_fastqc.html", + "WT_REP2_trimmed_2_val_2_fastqc.zip", + "multiqc", "star_salmon", - "WT_REP1", - "quant.sf", - "logs", - "salmon_quant.log", - "libParams", - "flenDist.txt", - "cmd_info.json", - "aux_info", - "fld.gz", - "observed_bias.gz", - "meta_info.json", - "expected_bias.gz", - "ambig_info.tsv", - "observed_bias_3p.gz", - "quant.genes.sf", - "salmon.merged.transcript_lengths.tsv", - "rseqc", - "bam_stat", - 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"WT_REP1.biotype_counts_mqc.tsv:md5,cac41767a8cc2e5fee58637971ec89d1", + "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", + "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", + "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", + "WT_REP1_dupMatrix.txt:md5,b6aa1b99d91f5fa7a94efeed1c496c00", + "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5", + "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79", + "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b", + "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043", + "WT_REP1_intercept_slope.txt:md5,e7fcac6d125a7ba746a5cba4a1e66aef", + "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,f3688a214d33a43ad79abe4b31df0c4b", + "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", + "RAP1_IAA_30M_REP1.featureCounts.txt:md5,b38da3230d4d29ebc8d4af36852d7212", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,d241d50e582ceb97e6f16b3556f5f5a9", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,2ab175746532de1c54020c1eabc27bb5", + "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,b621ce1e803d8670ece6c66391c33ba4", + "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", + "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,480b2586a878bc22f5b73f94051b41d8", + "WT_REP1.biotype_counts_mqc.tsv:md5,cac41767a8cc2e5fee58637971ec89d1", + "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", + "WT_REP1.featureCounts.txt:md5,112001ddbe917d935ee276d1685840bd", + "WT_REP2.biotype_counts_mqc.tsv:md5,e61b72317ac3c4d4ac64b663145e6262", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", - "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "WT_REP2.featureCounts.txt:md5,59e23ae18cfe6aa2e5a884bc03cbff15", - "WT_REP1.featureCounts.txt:md5,112001ddbe917d935ee276d1685840bd", - "WT_REP1_dupMatrix.txt:md5,b6aa1b99d91f5fa7a94efeed1c496c00", - "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5", - "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", - "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", - "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", - "WT_REP1_intercept_slope.txt:md5,e7fcac6d125a7ba746a5cba4a1e66aef", - "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e", - "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043", - "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b", - "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", - "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", - "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", - "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", - "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", - "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", - "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa", - "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", - "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", - "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", - "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", - "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", - "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", - "qualimap_gene_coverage_profile_Counts.txt:md5,02044ed1bf1eca19a8a87c9971cdc049", - "multiqc_featurecounts_biotype_plot.txt:md5,56be7f0813c3cbea0f68f61d9b355b71", - "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", - "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", - "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", - "qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", - "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", - "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c", - "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", - "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", - "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e", - "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0" + "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8", + "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", + "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", + "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3", + "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff", + "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff", + "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", + "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d", + "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d", + "coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1", + "coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211", + "coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211", + "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3", + "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b", + "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b", + "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,169d25b95c008bebe9ce886fea6a4e33", + "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,2ca0ce0fd3204bd2cc4812c4655b1f1f", + "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,7d5705880188f9beab1939e08d6b8f40", + "WT_REP1.infer_experiment.txt:md5,bf0c137f5fca06e7c40e1984a1acb06d", + "WT_REP2.infer_experiment.txt:md5,82e23b329ee60709f343bc2d17d43b14", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T11:26:28.121956" + "timestamp": "2024-09-17T12:34:14.672567" } } \ No newline at end of file diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index a0be2e956..f3dcf4cdc 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -17,7 +17,7 @@ class UTILS { if (matchesInclusion && matchesExclusion) output.add(file) } - return output + return output.sort { it.path } } // Static (global) exclusion regexes list From 6def0038cc8561e13798dc7a3501c8ae16e50442 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 17 Sep 2024 12:39:34 +0200 Subject: [PATCH 046/100] nf-core pipelines bump-version 3.16.0dev --- nextflow.config | 2 +- tests/default.nf.test.snap | 4 ++-- tests/featurecounts_group_type.nf.test.snap | 4 ++-- tests/hisat2.nf.test.snap | 4 ++-- tests/kallisto.nf.test.snap | 4 ++-- tests/min_mapped_reads.nf.test.snap | 4 ++-- tests/remove_ribo_rna.nf.test.snap | 4 ++-- tests/salmon.nf.test.snap | 4 ++-- tests/skip_qc.nf.test.snap | 4 ++-- tests/skip_trimming.nf.test.snap | 2 +- tests/star_rsem.nf.test.snap | 4 ++-- workflows/rnaseq/assets/multiqc/multiqc_config.yml | 2 +- 12 files changed, 21 insertions(+), 21 deletions(-) diff --git a/nextflow.config b/nextflow.config index d4bd05ca3..d5e00c6f4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -340,7 +340,7 @@ manifest { description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '3.15.1' + version = '3.16.0dev' doi = 'https://doi.org/10.5281/zenodo.1400710' } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index eb727b082..79b3ca290 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -266,7 +266,7 @@ }, "Params: default - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -932,7 +932,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 4bb12f76b..3a08ab907 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -747,7 +747,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", @@ -757,7 +757,7 @@ }, "Params: --featurecounts_group_type false - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 734ca3040..1a15dd9a4 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -631,7 +631,7 @@ }, "Params: --aligner hisat2 - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -726,7 +726,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_ALIGN={hisat2=2.2.1, samtools=1.16.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_ALIGN={hisat2=2.2.1, samtools=1.16.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index b0ff0b3fb..a431f33fc 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -103,7 +103,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, KALLISTO_QUANT={kallisto=0.48.0}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, KALLISTO_QUANT={kallisto=0.48.0}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", @@ -219,7 +219,7 @@ }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "multiqc_report.html", diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index c82193e9d..c68828368 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -447,7 +447,7 @@ }, "Params: --min_mapped_reads 90 - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -854,7 +854,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 64a3f6c91..a6e841b08 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -498,7 +498,7 @@ }, "Params: --remove_ribo_rna - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -954,7 +954,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, SORTMERNA={sortmerna=4.3.6}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, SORTMERNA={sortmerna=4.3.6}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 6ce551414..004c15ad4 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -61,7 +61,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", @@ -265,7 +265,7 @@ }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 7fcb8480a..7a1eaccf3 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -157,7 +157,7 @@ }, "Params: --skip_qc - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -477,7 +477,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index d40a54446..0cced5ad5 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -751,7 +751,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index db393113e..a6a804341 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -766,7 +766,7 @@ }, "Params: --aligner star_rsem - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -797,7 +797,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_RSEM={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEM_CALCULATEEXPRESSION={rsem=1.3.1, star=2.7.10a}, RSEM_MERGE_COUNTS={sed=4.7}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_RSEM={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEM_CALCULATEEXPRESSION={rsem=1.3.1, star=2.7.10a}, RSEM_MERGE_COUNTS={sed=4.7}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml index 47e347670..ff154e1cb 100644 --- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml +++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation. + This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: # Important checks and failures sample-status: From ca3a64633eb52c833850defba73ea80310236002 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 17 Sep 2024 14:23:55 +0200 Subject: [PATCH 047/100] update snapshots --- tests/featurecounts_group_type.nf.test.snap | 1940 +++++++++--------- tests/hisat2.nf.test.snap | 1752 ++++++++-------- tests/kallisto.nf.test.snap | 273 +-- tests/min_mapped_reads.nf.test.snap | 1666 +++++++-------- tests/remove_ribo_rna.nf.test.snap | 2048 ++++++++++--------- tests/salmon.nf.test.snap | 361 ++-- tests/skip_qc.nf.test.snap | 931 +++++---- tests/skip_trimming.nf.test.snap | 1850 +++++++++-------- tests/star_rsem.nf.test.snap | 1878 ++++++++--------- 9 files changed, 6479 insertions(+), 6220 deletions(-) diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 61c408139..9e142040a 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -42,43 +42,43 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.1" } }, [ + "custom", + "out", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", + "fastqc", + "raw", "RAP1_IAA_30M_REP1_raw.html", "RAP1_IAA_30M_REP1_raw.zip", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", "RAP1_UNINDUCED_REP1_raw.html", "RAP1_UNINDUCED_REP1_raw.zip", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", "RAP1_UNINDUCED_REP2_raw.html", "RAP1_UNINDUCED_REP2_raw.zip", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", "WT_REP1_raw.html", "WT_REP1_raw.zip", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", "WT_REP2_raw.html", "WT_REP2_raw.zip", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt", - "custom", - "fastqc", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", + "trim", "multiqc", + "star_salmon", "multiqc_data", "multiqc_plots", "multiqc_report.html", - "nf_core_rnaseq_software_mqc_versions.yml", - "out", "pipeline_info", - "raw", - "star_salmon", - "trim", - "trimgalore" + "nf_core_rnaseq_software_mqc_versions.yml", + "trimgalore", + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ @@ -88,7 +88,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T17:49:45.967217" + "timestamp": 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"lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", + "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", + "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", + "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", + "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", + "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", + "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", + "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", + "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], @@ -1245,6 +1275,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-14T09:47:53.335596" + "timestamp": "2024-09-17T12:54:59.807236" } } \ No 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"abundance.tsv:md5,a2c6108c384662f4da8c7b7fe8f27e02", + "abundance.tsv:md5,6fd77021287360f5005c90807233ab23", + "abundance.tsv:md5,7b62c5df0930e9f5ebc6e90d6aa600f6", + "abundance.tsv:md5,6fb211dc8e4fd238ca68d21d6cc83cf5", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -241,15 +247,14 @@ "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" + "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804" ] ], "meta": { "nf-test": "0.9.0", "nextflow": 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"RAP1_IAA_30M_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", + "RAP1_IAA_30M_REP1.coverage.gtf", + "RAP1_IAA_30M_REP1.gene.abundance.txt", + "RAP1_IAA_30M_REP1.transcripts.gtf", + "RAP1_UNINDUCED_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", + "RAP1_UNINDUCED_REP1.coverage.gtf", + "RAP1_UNINDUCED_REP1.gene.abundance.txt", + "RAP1_UNINDUCED_REP1.transcripts.gtf", + "RAP1_UNINDUCED_REP2.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", + "RAP1_UNINDUCED_REP2.coverage.gtf", + "RAP1_UNINDUCED_REP2.gene.abundance.txt", + "RAP1_UNINDUCED_REP2.transcripts.gtf", + "WT_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", + "WT_REP1.coverage.gtf", + "WT_REP1.gene.abundance.txt", + "WT_REP1.transcripts.gtf", + "WT_REP2.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", - "trim", - "trimgalore", - "tx2gene.tsv", + "WT_REP2.coverage.gtf", + "WT_REP2.gene.abundance.txt", + "WT_REP2.transcripts.gtf", "tx2gene.tsv", - "txt", - "underscore.js", - "underscore.js", - "underscore.js", - "underscore.js", - "underscore.js", - "up-pressed.png", - "up-pressed.png", - "up-pressed.png", - "up-pressed.png", - "up-pressed.png", - "up.png", - "up.png", - "up.png", - "up.png", - "up.png", - "websupport.js", - "websupport.js", - "websupport.js", - "websupport.js", - "websupport.js", - "xls", - "xls" + "trimgalore", + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ - 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"RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,1c9d07d9f9d12219d2b9f761f854eced", - "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", - "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,de016e691f5d56b13bbaa626ce2cc93e", - "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,484e2860c6c496b1da5fac475a0cd3e4", - "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,c0bf1135d2d70c5918d87f706c0c54bc", - "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,c3900f3bb24cd339d0e0ecf65ae43217", - "WT_REP1.biotype_counts_mqc.tsv:md5,eca4a76b9243248d01df5f4289b8201e", - "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", - "WT_REP1.featureCounts.txt:md5,7aadafd0a26f5047a9ae7266eccfce05", - "WT_REP1.infer_experiment.txt:md5,298c430c61cb7a46b48af867a0dfe00b", - "WT_REP1_dupMatrix.txt:md5,b0de1683f2a9bfa42437e924a11648fd", - "WT_REP1_intercept_slope.txt:md5,f38c8525b7fcb990b7158f1518e451ad", - "WT_REP2.biotype_counts_mqc.tsv:md5,530605b80da27915a90d452249f3243a", - "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", - "WT_REP2.featureCounts.txt:md5,809af01851125c401d576c21efca7b5a", - "WT_REP2.infer_experiment.txt:md5,18758f433cf5c19bce599e5329da39a9", - "WT_REP2_dupMatrix.txt:md5,bab18079153627205e5d907d8dfba677", - "WT_REP2_intercept_slope.txt:md5,9bcbc18d0d331fe3c972538456ffd5b2", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -1294,7 +1264,77 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,53addd7b78d8ae224920ec9b97489d72", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,97fc7bde65a7efc5ab3af48ef0400c20", + "ambig_info.tsv:md5,25ced9693254994a7878241225baabb6", + "cmd_info.json:md5,306609f606004616a89ec50dc59f22b0", + "lib_format_counts.json:md5,b814fed52bd197a64544086dba0f127a", + "ambig_info.tsv:md5,c83b0f9ebe9b8dfc284595ec56d4f092", + "cmd_info.json:md5,6b367a9cdd2837b88890209459acf45f", + "lib_format_counts.json:md5,3f4d67ace359562564dd336aa47a479c", + "ambig_info.tsv:md5,00a1f9de7095a68dfb43e0a0301b6ecd", + "cmd_info.json:md5,c8c6208e1082ec150de56679b2b8cfe3", + "lib_format_counts.json:md5,f56087bcbd494c7fa78200f65a2400e2", + "ambig_info.tsv:md5,54d942ddf69b4e8f1598064e09428256", + "cmd_info.json:md5,5523405c02d30489d276e5d734cb54da", + "lib_format_counts.json:md5,43fc5463eada79e466d6ba9848739f06", + "ambig_info.tsv:md5,933feffdaf6cf6ff407469ade0d7684d", + "cmd_info.json:md5,998c89efb00fa5e63fd1d18c0602a019", + "lib_format_counts.json:md5,e6e3d7746e9abee6a0e097ae0ee1781a", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", + "ambig_info.tsv:md5,6cd02367152bb2dd59a6f1f70df2d7f8", + "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "ambig_info.tsv:md5,8611b6c03f6aa1a5f3dfceb0e65ad4ef", + "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "ambig_info.tsv:md5,1b69f9b651dfa6799e310004c1e3309f", + "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "ambig_info.tsv:md5,070c7d50eab5ce0f211cdb06f9d7cc29", + "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "ambig_info.tsv:md5,b8c61854b56a1c9a0fc8f158ea0c7599", + "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,ddadea4a08511aae6faeb632eb6aafea", + "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,1db4c86723cf69052c4386760a9750bb", + "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,c0bf1135d2d70c5918d87f706c0c54bc", + "WT_REP1_dupMatrix.txt:md5,b0de1683f2a9bfa42437e924a11648fd", + "WT_REP2_dupMatrix.txt:md5,bab18079153627205e5d907d8dfba677", + "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,b21a53b0156b0afdfc28c237cb11218d", + "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,eccc5ca37855c717d35477e684188695", + "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,c3900f3bb24cd339d0e0ecf65ae43217", + "WT_REP1_intercept_slope.txt:md5,f38c8525b7fcb990b7158f1518e451ad", + "WT_REP2_intercept_slope.txt:md5,9bcbc18d0d331fe3c972538456ffd5b2", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,f36792d25b268b6d556f8728300f4afc", + "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", + "RAP1_IAA_30M_REP1.featureCounts.txt:md5,c5865ded7168476d93057d2aedaec694", + "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,782f5001d411ba79314ba77f7d36b157", + "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", + "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,a0fb30c2b937a5a41ac865ab09367af7", + "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,1c9d07d9f9d12219d2b9f761f854eced", + "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", + "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,de016e691f5d56b13bbaa626ce2cc93e", + "WT_REP1.biotype_counts_mqc.tsv:md5,eca4a76b9243248d01df5f4289b8201e", + "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", + "WT_REP1.featureCounts.txt:md5,7aadafd0a26f5047a9ae7266eccfce05", + "WT_REP2.biotype_counts_mqc.tsv:md5,530605b80da27915a90d452249f3243a", + "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", + "WT_REP2.featureCounts.txt:md5,809af01851125c401d576c21efca7b5a", + "coverage_profile_along_genes_(high).txt:md5,5aee6c959137a8c9bfbd0ddaa79dddba", + "coverage_profile_along_genes_(low).txt:md5,d2742410803e0de7cc606ef118010ea8", + "coverage_profile_along_genes_(total).txt:md5,d2742410803e0de7cc606ef118010ea8", + "coverage_profile_along_genes_(high).txt:md5,f5ac8f74fcad5d9ac72dbb6b65184bd0", + "coverage_profile_along_genes_(low).txt:md5,d66da6e3f49b0870184fc881a162e785", + "coverage_profile_along_genes_(total).txt:md5,d66da6e3f49b0870184fc881a162e785", + "coverage_profile_along_genes_(high).txt:md5,634f447f91db940d2148af74cf36febd", + "coverage_profile_along_genes_(low).txt:md5,db2e0acbe9f07c68bcd7e08e036f02d3", + "coverage_profile_along_genes_(total).txt:md5,db2e0acbe9f07c68bcd7e08e036f02d3", + "coverage_profile_along_genes_(high).txt:md5,a349232d75f6c0adab6afcd9f6cbbafb", + "coverage_profile_along_genes_(low).txt:md5,b2c696661e6c524b1641eb7267c70edc", + "coverage_profile_along_genes_(total).txt:md5,b2c696661e6c524b1641eb7267c70edc", + "coverage_profile_along_genes_(high).txt:md5,3f76529bd723d5320c86cc407fbb3294", + "coverage_profile_along_genes_(low).txt:md5,b9be191fdec82c78057e083d3adf20dd", + "coverage_profile_along_genes_(total).txt:md5,b9be191fdec82c78057e083d3adf20dd", + "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,ee69422d6e76fba223aa6b20a13027d2", + "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,ec9ec42ddfd3ffbb5373d3d6b6713b2c", + "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,484e2860c6c496b1da5fac475a0cd3e4", + "WT_REP1.infer_experiment.txt:md5,298c430c61cb7a46b48af867a0dfe00b", + "WT_REP2.infer_experiment.txt:md5,18758f433cf5c19bce599e5329da39a9", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], @@ -1302,7 +1342,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-14T10:03:34.943643" + "timestamp": "2024-09-17T13:18:05.873394" }, "Params: --remove_ribo_rna - stub": { "content": [ @@ -1350,43 +1390,43 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.1" } }, [ + "custom", + "out", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", + "fastqc", + "raw", "RAP1_IAA_30M_REP1_raw.html", "RAP1_IAA_30M_REP1_raw.zip", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", "RAP1_UNINDUCED_REP1_raw.html", "RAP1_UNINDUCED_REP1_raw.zip", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", "RAP1_UNINDUCED_REP2_raw.html", "RAP1_UNINDUCED_REP2_raw.zip", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", "WT_REP1_raw.html", "WT_REP1_raw.zip", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", "WT_REP2_raw.html", "WT_REP2_raw.zip", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt", - "custom", - "fastqc", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", + "trim", "multiqc", + "star_salmon", "multiqc_data", "multiqc_plots", "multiqc_report.html", - "nf_core_rnaseq_software_mqc_versions.yml", - "out", "pipeline_info", - "raw", - "star_salmon", - "trim", - "trimgalore" + "nf_core_rnaseq_software_mqc_versions.yml", + "trimgalore", + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ @@ -1396,6 +1436,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-14T10:04:28.342005" + "timestamp": "2024-09-17T13:18:51.223833" } } \ No newline at end of file diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 89342b2fc..73abab293 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -49,202 +49,205 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.1" } }, [ - "RAP1_IAA_30M_REP1", + "bbsplit", "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1.stats.txt", + "RAP1_UNINDUCED_REP2.stats.txt", + "WT_REP1.stats.txt", + "WT_REP2.stats.txt", + "custom", + "out", + "genome_gfp.fasta", + "genome_gfp.gtf", + "fastqc", + "trim", "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", - "RAP1_UNINDUCED_REP1", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", - "RAP1_UNINDUCED_REP2", - "RAP1_UNINDUCED_REP2.stats.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", - "WT_REP1", - "WT_REP1.stats.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", "WT_REP1_trimmed_1_val_1_fastqc.html", "WT_REP1_trimmed_1_val_1_fastqc.zip", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", "WT_REP1_trimmed_2_val_2_fastqc.html", "WT_REP1_trimmed_2_val_2_fastqc.zip", - "WT_REP2", - "WT_REP2.stats.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", "WT_REP2_trimmed_1_val_1_fastqc.html", "WT_REP2_trimmed_1_val_1_fastqc.zip", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt", "WT_REP2_trimmed_2_val_2_fastqc.html", "WT_REP2_trimmed_2_val_2_fastqc.zip", - "ambig_info.tsv", - "ambig_info.tsv", - "ambig_info.tsv", - "ambig_info.tsv", - "ambig_info.tsv", - "aux_info", - "aux_info", - "aux_info", - "aux_info", - "aux_info", - "bbsplit", - "cmd_info.json", - "cmd_info.json", - "cmd_info.json", - "cmd_info.json", - "cmd_info.json", - "custom", - "cutadapt_filtered_reads_plot-cnt.pdf", - "cutadapt_filtered_reads_plot-cnt.png", - "cutadapt_filtered_reads_plot-cnt.svg", - "cutadapt_filtered_reads_plot-pct.pdf", - "cutadapt_filtered_reads_plot-pct.png", - "cutadapt_filtered_reads_plot-pct.svg", + "multiqc", + "multiqc_report.html", + "multiqc_report_data", "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.pdf", - "cutadapt_trimmed_sequences_plot_3_Counts.png", - "cutadapt_trimmed_sequences_plot_3_Counts.svg", "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "expected_bias.gz", - "expected_bias.gz", - "expected_bias.gz", - "expected_bias.gz", - "expected_bias.gz", - "fastqc", - "fastqc-status-check-heatmap.pdf", - "fastqc-status-check-heatmap.png", - "fastqc-status-check-heatmap.svg", "fastqc-status-check-heatmap.txt", - "fastqc_overrepresented_sequences_plot.pdf", - "fastqc_overrepresented_sequences_plot.png", - "fastqc_overrepresented_sequences_plot.svg", "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot.pdf", - "fastqc_per_base_n_content_plot.png", - "fastqc_per_base_n_content_plot.svg", "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot.pdf", - "fastqc_per_base_sequence_quality_plot.png", - "fastqc_per_base_sequence_quality_plot.svg", "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot_Counts.pdf", - "fastqc_per_sequence_gc_content_plot_Counts.png", - "fastqc_per_sequence_gc_content_plot_Counts.svg", "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "fastqc_per_sequence_gc_content_plot_Percentages.png", - "fastqc_per_sequence_gc_content_plot_Percentages.svg", "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot.pdf", - "fastqc_per_sequence_quality_scores_plot.png", - "fastqc_per_sequence_quality_scores_plot.svg", "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot-cnt.pdf", - "fastqc_sequence_counts_plot-cnt.png", - "fastqc_sequence_counts_plot-cnt.svg", - "fastqc_sequence_counts_plot-pct.pdf", - "fastqc_sequence_counts_plot-pct.png", - "fastqc_sequence_counts_plot-pct.svg", "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot.pdf", - "fastqc_sequence_duplication_levels_plot.png", - "fastqc_sequence_duplication_levels_plot.svg", "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.pdf", - "fastqc_sequence_length_distribution_plot.png", - "fastqc_sequence_length_distribution_plot.svg", "fastqc_sequence_length_distribution_plot.txt", - "fastqc_top_overrepresented_sequences_table.pdf", - "fastqc_top_overrepresented_sequences_table.png", - "fastqc_top_overrepresented_sequences_table.svg", "fastqc_top_overrepresented_sequences_table.txt", - "fld.gz", - "fld.gz", - "fld.gz", - "fld.gz", - "fld.gz", - "flenDist.txt", - "flenDist.txt", - "flenDist.txt", - "flenDist.txt", - "flenDist.txt", - "general_stats_table.pdf", - "general_stats_table.png", - "general_stats_table.svg", - "genome_gfp.fasta", - "genome_gfp.gtf", - "libParams", - "libParams", - "libParams", - "libParams", - "libParams", - "lib_format_counts.json", - "lib_format_counts.json", - "lib_format_counts.json", - "lib_format_counts.json", - "lib_format_counts.json", - "logs", - "logs", - "logs", - "logs", - "logs", - "meta_info.json", - "meta_info.json", - "meta_info.json", - "meta_info.json", - "meta_info.json", - "multiqc", "multiqc_citations.txt", "multiqc_cutadapt.txt", "multiqc_data.json", "multiqc_fastqc_fastqc_trimmed.txt", "multiqc_general_stats.txt", - "multiqc_report.html", - "multiqc_report_data", - "multiqc_report_plots", "multiqc_salmon.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", + "salmon_plot.txt", + "multiqc_report_plots", + "pdf", + "cutadapt_filtered_reads_plot-cnt.pdf", + "cutadapt_filtered_reads_plot-pct.pdf", + "cutadapt_trimmed_sequences_plot_3_Counts.pdf", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf", + "general_stats_table.pdf", + "salmon_plot.pdf", + "png", + "cutadapt_filtered_reads_plot-cnt.png", + "cutadapt_filtered_reads_plot-pct.png", + "cutadapt_trimmed_sequences_plot_3_Counts.png", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png", + "general_stats_table.png", + "salmon_plot.png", + "svg", + "cutadapt_filtered_reads_plot-cnt.svg", + "cutadapt_filtered_reads_plot-pct.svg", + "cutadapt_trimmed_sequences_plot_3_Counts.svg", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg", + "general_stats_table.svg", + "salmon_plot.svg", + "pipeline_info", "nf_core_rnaseq_software_mqc_versions.yml", + "salmon", + "RAP1_IAA_30M_REP1", + "aux_info", + "ambig_info.tsv", + "expected_bias.gz", + "fld.gz", + "meta_info.json", "observed_bias.gz", - "observed_bias.gz", - "observed_bias.gz", - "observed_bias.gz", - "observed_bias.gz", - "observed_bias_3p.gz", - "observed_bias_3p.gz", - "observed_bias_3p.gz", "observed_bias_3p.gz", - "observed_bias_3p.gz", - "out", - "pdf", - "pipeline_info", - "png", - "quant.genes.sf", - "quant.genes.sf", - "quant.genes.sf", - "quant.genes.sf", + "cmd_info.json", + "libParams", + "flenDist.txt", + "lib_format_counts.json", + "logs", + "salmon_quant.log", "quant.genes.sf", "quant.sf", + "RAP1_UNINDUCED_REP1", + "aux_info", + "ambig_info.tsv", + "expected_bias.gz", + "fld.gz", + "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", + "libParams", + "flenDist.txt", + "lib_format_counts.json", + "logs", + "salmon_quant.log", + "quant.genes.sf", "quant.sf", + "RAP1_UNINDUCED_REP2", + "aux_info", + "ambig_info.tsv", + "expected_bias.gz", + "fld.gz", + "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", + "libParams", + "flenDist.txt", + "lib_format_counts.json", + "logs", + "salmon_quant.log", + "quant.genes.sf", "quant.sf", + "WT_REP1", + "aux_info", + "ambig_info.tsv", + "expected_bias.gz", + "fld.gz", + "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", + "libParams", + "flenDist.txt", + "lib_format_counts.json", + "logs", + "salmon_quant.log", + "quant.genes.sf", "quant.sf", + "WT_REP2", + "aux_info", + "ambig_info.tsv", + "expected_bias.gz", + "fld.gz", + "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", + "libParams", + "flenDist.txt", + "lib_format_counts.json", + "logs", + "salmon_quant.log", + "quant.genes.sf", "quant.sf", - "salmon", "salmon.merged.gene_counts.SummarizedExperiment.rds", "salmon.merged.gene_counts.tsv", "salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds", @@ -257,19 +260,16 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", - "salmon_plot.pdf", - "salmon_plot.png", - "salmon_plot.svg", - "salmon_plot.txt", - "salmon_quant.log", - "salmon_quant.log", - "salmon_quant.log", - "salmon_quant.log", - "salmon_quant.log", - "svg", - "trim", + "tx2gene.tsv", "trimgalore", - "tx2gene.tsv" + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", @@ -288,6 +288,21 @@ "multiqc_citations.txt:md5,f789abe663d4b4214f0ddeb413a7f150", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", + "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", + "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", + "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", + "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", + "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", + "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", + "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", + "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", + "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", + "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], @@ -295,7 +310,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T20:04:29.708154" + "timestamp": "2024-09-17T13:21:46.987509" }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ @@ -332,31 +347,31 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.1" } }, [ - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt", "custom", - "fastqc", + "out", "genome_transcriptome.fasta", "genome_transcriptome.gtf", + "fastqc", + "trim", "multiqc", "multiqc_data", "multiqc_plots", "multiqc_report.html", - "nf_core_rnaseq_software_mqc_versions.yml", - "out", "pipeline_info", - "trim", - "trimgalore" + "nf_core_rnaseq_software_mqc_versions.yml", + "trimgalore", + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ @@ -366,6 +381,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T18:37:06.985778" + "timestamp": "2024-09-17T13:22:21.275937" } } \ No newline at end of file diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 1d9778367..bb5be7bfd 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -39,32 +39,32 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.1" } }, [ - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt", "custom", - "fastqc", + "out", "genome_transcriptome.fasta", "genome_transcriptome.gtf", + "fastqc", + "trim", "multiqc", + "star_salmon", "multiqc_data", "multiqc_plots", "multiqc_report.html", - "nf_core_rnaseq_software_mqc_versions.yml", - "out", "pipeline_info", - "star_salmon", - "trim", - "trimgalore" + "nf_core_rnaseq_software_mqc_versions.yml", + "trimgalore", + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ @@ -74,7 +74,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T18:45:06.0114" + "timestamp": "2024-09-17T13:28:26.396195" }, "Params: --skip_qc": { "content": [ @@ -166,341 +166,62 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.1" } }, [ - "RAP1_IAA_30M_REP1", - "RAP1_IAA_30M_REP1", - "RAP1_IAA_30M_REP1.Log.final.out", - "RAP1_IAA_30M_REP1.Log.out", - "RAP1_IAA_30M_REP1.Log.progress.out", - "RAP1_IAA_30M_REP1.SJ.out.tab", - "RAP1_IAA_30M_REP1.ballgown", - "RAP1_IAA_30M_REP1.coverage.gtf", - "RAP1_IAA_30M_REP1.forward.bigWig", - "RAP1_IAA_30M_REP1.gene.abundance.txt", - "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", - "RAP1_IAA_30M_REP1.markdup.sorted.bam", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", - "RAP1_IAA_30M_REP1.reverse.bigWig", - "RAP1_IAA_30M_REP1.sorted.bam.flagstat", - "RAP1_IAA_30M_REP1.sorted.bam.idxstats", - "RAP1_IAA_30M_REP1.sorted.bam.stats", + 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"lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", + "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", + "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", + "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", + "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", + "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", + "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", + "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", + "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", + "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", + 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"WT_REP1.biotype_counts_mqc.tsv:md5,512645a8f736eee160c4465e1940f4a5", - "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", - "WT_REP1.featureCounts.txt:md5,289cc95971a3ec550e018659279c1f59", - "WT_REP1.infer_experiment.txt:md5,d55921c0084806cdf49b9bd8653c8e09", - "WT_REP1_dupMatrix.txt:md5,802dd0de10d9118943869239f8659c78", - "WT_REP1_intercept_slope.txt:md5,9c2e2b7890427e79c97e65827102d965", - "WT_REP2.biotype_counts_mqc.tsv:md5,d4957c0197636b68d27fbd60d388bba1", - "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", - "WT_REP2.featureCounts.txt:md5,152d2f26df56a88fe4b27c742d8f7447", - "WT_REP2.infer_experiment.txt:md5,fe87600c55f433ba995fe18bed5cf5f1", - "WT_REP2_dupMatrix.txt:md5,e97a3c8d2e606d7d4b40cd33eb0b96c4", - "WT_REP2_intercept_slope.txt:md5,db7a36459f2036de6657e74d2c98a47c", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -1207,22 +1177,82 @@ "qualimap_gene_coverage_profile_Counts.txt:md5,387c07f2a93e3d13048c4cd788d1fcc3", "qualimap_gene_coverage_profile_Normalised.txt:md5,35f0b71796622269bc51cf1e7a0650ab", "qualimap_rnaseq_cov_hist.txt:md5,a620cb9d1878e86e10e87500e98122f1", - "rsem.merged.gene_counts.tsv:md5,47f272199f24af4473c959df2a9149dc", - "rsem.merged.gene_tpm.tsv:md5,a197b2d131dea75a83f9c219c23fb7a0", - "rsem.merged.transcript_counts.tsv:md5,ffc75fd409d75edf5209e8e1af8ec8fc", - "rsem.merged.transcript_tpm.tsv:md5,b836618c69d111edf635ce7244ee85e5", "rseqc_infer_experiment_plot.txt:md5,c0ddf72b026cdc54ad03e75eaa636f7e", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3e67e07b5c978fa363965e8e90356eef", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,a83e44c5a22e014d377c41419175784c", - "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" + "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", + "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", + "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", + "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", + "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", + "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", + "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", + "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", + "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", + "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", + "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,8da31020df3c5b25167345609c6d08c5", + "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,3f269a6b2e9c8eaab66582e31d208dfc", + "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,7d96d6ddf1d12d43837b105865aeaafa", + "WT_REP1_dupMatrix.txt:md5,802dd0de10d9118943869239f8659c78", + "WT_REP2_dupMatrix.txt:md5,e97a3c8d2e606d7d4b40cd33eb0b96c4", + "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,d280fe126a5e82d24121d8662fd5a161", + "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,a498640b0f9e710311ebc3eb67cedbd0", + "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,a1c5346e3bad40546c793b8914a22e7e", + "WT_REP1_intercept_slope.txt:md5,9c2e2b7890427e79c97e65827102d965", + "WT_REP2_intercept_slope.txt:md5,db7a36459f2036de6657e74d2c98a47c", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,e66cd2b584d970ae3827ad2521f795ca", + "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", + "RAP1_IAA_30M_REP1.featureCounts.txt:md5,b3013c797d2fd38a8efa39047f5ba1b1", + "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,548023e639f8eb76f973a2f98bcbc82c", + "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", + "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,ff59317794fc04d5a4fd18797f0ecb0f", + "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,2c0b5696582493f7a50259679982a6b3", + "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", + "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,6ee84531ba255791a11b487b6aea75ab", + "WT_REP1.biotype_counts_mqc.tsv:md5,512645a8f736eee160c4465e1940f4a5", + "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", + "WT_REP1.featureCounts.txt:md5,289cc95971a3ec550e018659279c1f59", + "WT_REP2.biotype_counts_mqc.tsv:md5,d4957c0197636b68d27fbd60d388bba1", + "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", + "WT_REP2.featureCounts.txt:md5,152d2f26df56a88fe4b27c742d8f7447", + "coverage_profile_along_genes_(high).txt:md5,31ab137e75752225365bd3d89143dbd2", + "coverage_profile_along_genes_(low).txt:md5,eaceda909bf652b8301fa0ed1bba9ae1", + "coverage_profile_along_genes_(total).txt:md5,eaceda909bf652b8301fa0ed1bba9ae1", + "coverage_profile_along_genes_(high).txt:md5,93822686a53dd40d3ff426ddbfc9314e", + "coverage_profile_along_genes_(low).txt:md5,bd8d58c757e4122caee4b4e8df2f4b00", + "coverage_profile_along_genes_(total).txt:md5,bd8d58c757e4122caee4b4e8df2f4b00", + "coverage_profile_along_genes_(high).txt:md5,cdb2c00c43121e3beccd7f670b34e05e", + "coverage_profile_along_genes_(low).txt:md5,1a9405c8bd7c00f3be082bfebb90b6ed", + "coverage_profile_along_genes_(total).txt:md5,1a9405c8bd7c00f3be082bfebb90b6ed", + "coverage_profile_along_genes_(high).txt:md5,70c95fbc100f14911d2cc348bdff1587", + "coverage_profile_along_genes_(low).txt:md5,86e56ef794277bcf1e0d121a088b8581", + "coverage_profile_along_genes_(total).txt:md5,86e56ef794277bcf1e0d121a088b8581", + "coverage_profile_along_genes_(high).txt:md5,a73462b9ecbd1d2c45d7ca84b5f7925b", + "coverage_profile_along_genes_(low).txt:md5,7adc228bc15e344abb7938ea4d35a846", + "coverage_profile_along_genes_(total).txt:md5,7adc228bc15e344abb7938ea4d35a846", + "rsem.merged.gene_counts.tsv:md5,47f272199f24af4473c959df2a9149dc", + "rsem.merged.gene_tpm.tsv:md5,a197b2d131dea75a83f9c219c23fb7a0", + "rsem.merged.transcript_counts.tsv:md5,ffc75fd409d75edf5209e8e1af8ec8fc", + "rsem.merged.transcript_tpm.tsv:md5,b836618c69d111edf635ce7244ee85e5", + "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,1f31ddae1f98e779e30d846cde3834de", + "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,a2a8e31dbd0ebd0c12f3f968ffd5391b", + "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,9ec058d3a4162fd1b4c6175e2106eef4", + "WT_REP1.infer_experiment.txt:md5,d55921c0084806cdf49b9bd8653c8e09", + "WT_REP2.infer_experiment.txt:md5,fe87600c55f433ba995fe18bed5cf5f1" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T22:42:21.244724" + "timestamp": "2024-09-17T13:41:27.82476" }, "Params: --aligner star_rsem - stub": { "content": [ @@ -1265,43 +1295,43 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.1" } }, [ + "custom", + "out", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", + "fastqc", + "raw", "RAP1_IAA_30M_REP1_raw.html", "RAP1_IAA_30M_REP1_raw.zip", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", "RAP1_UNINDUCED_REP1_raw.html", "RAP1_UNINDUCED_REP1_raw.zip", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", "RAP1_UNINDUCED_REP2_raw.html", "RAP1_UNINDUCED_REP2_raw.zip", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", "WT_REP1_raw.html", "WT_REP1_raw.zip", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", "WT_REP2_raw.html", "WT_REP2_raw.zip", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt", - "custom", - "fastqc", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", + "trim", "multiqc", + "star_rsem", "multiqc_data", "multiqc_plots", "multiqc_report.html", - "nf_core_rnaseq_software_mqc_versions.yml", - "out", "pipeline_info", - "raw", - "star_rsem", - "trim", - "trimgalore" + "nf_core_rnaseq_software_mqc_versions.yml", + "trimgalore", + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ @@ -1311,6 +1341,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T19:01:09.265956" + "timestamp": "2024-09-17T13:42:16.948827" } } \ No newline at end of file From 85b320b60f42d3468434095ee1464460abe63ab9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 17 Sep 2024 14:25:46 +0200 Subject: [PATCH 048/100] update CHANGELOG --- CHANGELOG.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index cd24663bd..e693e7f7e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## dev + +### Enhancements & fixes + +- [PR #1186](https://github.com/nf-core/rnaseq/pull/1186) - Bump pipeline version to 3.16.0dev + ## [[3.15.1](https://github.com/nf-core/rnaseq/releases/tag/3.15.1)] - 2024-09-16 ### Enhancements & fixes From 6ea73a6768585128e6c08bf6080e81a27bca1a98 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 17 Sep 2024 14:39:04 +0200 Subject: [PATCH 049/100] Update CHANGELOG.md Co-authored-by: Jonathan Manning --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e693e7f7e..916c78035 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## dev +## v3.16.0dev - [date] ### Enhancements & fixes From 17054a4b8cc9d2a1f77429e721b2c5937c227d5a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 17 Sep 2024 15:26:39 +0200 Subject: [PATCH 050/100] snapshot more files --- tests/default.nf.test.snap | 182 ++++++++++++++++++++++++++++++++++++- tests/lib/UTILS.groovy | 27 ++---- 2 files changed, 186 insertions(+), 23 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 3c2319ca0..5c2fa7035 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -81,14 +81,15 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ - + "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T12:25:22.192471" + "timestamp": "2024-09-17T15:25:48.810875" }, "Params: default": { "content": [ @@ -1296,6 +1297,8 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ + "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", + "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -1335,32 +1338,95 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", + "dupradar-section-plot.png:md5,3ae5e5cb161b7abd878d718bc71b41f6", + "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890", + "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84", + "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f", + "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14", + "fastqc_per_sequence_gc_content_plot-1_Counts.png:md5,8a806cec2142f9911502e0a253d83d13", + "fastqc_per_sequence_gc_content_plot-1_Percentages.png:md5,953929d50c8490029880e205e4db7959", + "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16", + "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,eba3abf8bedb2cb20bad90c54e9c8881", + "fastqc_per_sequence_quality_scores_plot-1.png:md5,d2c29cae169f35744500c751b4a7366e", + "fastqc_per_sequence_quality_scores_plot.png:md5,42fd7369a8aca78f620164a9e887c3cb", + "fastqc_sequence_counts_plot-1-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", + "fastqc_sequence_counts_plot-1-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", + "fastqc_sequence_counts_plot-cnt.png:md5,3890d5555f2a39b46b9f6efb14cb91f2", + "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054", + 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"coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3", "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b", "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b", @@ -1406,6 +1562,26 @@ "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,7d5705880188f9beab1939e08d6b8f40", "WT_REP1.infer_experiment.txt:md5,bf0c137f5fca06e7c40e1984a1acb06d", "WT_REP2.infer_experiment.txt:md5,82e23b329ee60709f343bc2d17d43b14", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,3f149502efe2a9d4bac98b1dd18c15e7", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,a052ab04070e72cc318fb7680b0764e3", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,e82329a443b9ff50a86e42aff91bd704", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,d279003d92f7feef9adb31203f84474a", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,10e2d00f93f9e74f224bd3c1bfbeb29b", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,9aa371befc36478d7720d3ea275e6f4d", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,907ab2e06346df131cbdb929afc005a8", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,b03f3118d1aa58fceadcb3311028e856", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,041edee3193df311f621c09f4991892b", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], @@ -1413,6 +1589,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T12:34:14.672567" + "timestamp": "2024-09-17T15:24:24.41718" } } \ No newline at end of file diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index f3dcf4cdc..4ff001eb4 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -22,7 +22,7 @@ class UTILS { // Static (global) exclusion regexes list static List exclusionRegexesForUnstableFileNames = [/.*\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}.*/] - static List snapshottablePatterns = [/.*\.(txt|json|tsv)$/] + static List snapshottablePatterns = [/.*\.(ctab|fasta|gtf|gz|json|log|png|tab|tsv|txt)$/] static List exclusionRegexesForUnstableFileContents = [ // To exclude files with timestamps in the format YYYY-MM-DD_HH-MM-SS /\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}/, @@ -30,28 +30,15 @@ class UTILS { // To exlude bbsplit files /.*\.stats\.txt/, - // To exclude fastqc files - /.*_fastqc\.html/, - /.*_fastqc\.zip/, - // To exclude from the MultiQC reports - /cutadapt_filtered_reads_plot-cnt\.pdf/, - /cutadapt_filtered_reads_plot-cnt\.svg/, - /cutadapt_filtered_reads_plot-pct\.pdf/, - /cutadapt_filtered_reads_plot-pct\.svg/, - /cutadapt_trimmed_sequences_plot_3_Counts\.pdf/, - /cutadapt_trimmed_sequences_plot_3_Counts\.svg/, - /cutadapt_trimmed_sequences_plot_3_Obs_Exp\.pdf/, - /cutadapt_trimmed_sequences_plot_3_Obs_Exp\.svg/, + /cutadapt_filtered_reads_plot-.*/, + /cutadapt_trimmed_sequences_.*\.pdf/, + /cutadapt_trimmed_sequences_.*\.svg/, /dupradar-section-plot\.pdf/, /dupradar-section-plot\.svg/, - /fail_strand_check_table\.pdf/, - /fail_strand_check_table\.png/, - /fail_strand_check_table\.svg/, - /fastqc-status-check-heatmap-1\.pdf/, - /fastqc-status-check-heatmap-1\.svg/, - /fastqc-status-check-heatmap\.pdf/, - /fastqc-status-check-heatmap\.svg/, + /fail_strand_check_table.*/, + /fastqc-status-check-.*\.pdf/, + /fastqc-status-check-.*\.svg/, /fastqc_adapter_content_plot\.pdf/, /fastqc_adapter_content_plot\.png/, /fastqc_adapter_content_plot\.svg/, From 5b41e56ce6df20f757ee1f587e17ba55ddf689e0 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 17 Sep 2024 22:58:09 +0200 Subject: [PATCH 051/100] snapshot more files --- tests/default.nf.test | 19 +- tests/default.nf.test.snap | 294 +--------------- tests/hisat2.nf.test | 18 +- tests/hisat2.nf.test.snap | 458 ++++++++++--------------- tests/kallisto.nf.test | 18 +- tests/kallisto.nf.test.snap | 85 ++--- tests/lib/UTILS.groovy | 25 +- tests/min_mapped_reads.nf.test | 18 +- tests/min_mapped_reads.nf.test.snap | 381 ++++++++------------- tests/remove_ribo_rna.nf.test | 18 +- tests/remove_ribo_rna.nf.test.snap | 498 +++++++++++----------------- tests/salmon.nf.test | 18 +- tests/salmon.nf.test.snap | 101 ++---- tests/skip_qc.nf.test | 18 +- tests/skip_qc.nf.test.snap | 211 +++++------- tests/skip_trimming.nf.test | 9 +- tests/skip_trimming.nf.test.snap | 434 ++++++++++-------------- tests/star_rsem.nf.test | 18 +- tests/star_rsem.nf.test.snap | 477 ++++++++++---------------- 19 files changed, 1125 insertions(+), 1993 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index e641012c5..829d4471c 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -12,15 +12,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } @@ -37,15 +38,17 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + + def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 5c2fa7035..3869a8acf 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,6 +1,7 @@ { "Params: default - stub": { "content": [ + 22, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -48,8 +49,6 @@ [ "custom", "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw.html", @@ -89,10 +88,11 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T15:25:48.810875" + "timestamp": "2024-09-17T18:13:03.370736" }, "Params: default": { "content": [ + 198, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -237,8 +237,6 @@ "WT_REP2.stats.txt", "custom", "out", - "genome_gfp.fasta", - "genome_gfp.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw_1_fastqc.html", @@ -278,41 +276,13 @@ "star_salmon", "multiqc_report.html", "multiqc_report_data", - "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "fastqc-status-check-heatmap-1.txt", - "fastqc-status-check-heatmap.txt", - "fastqc_adapter_content_plot.txt", - "fastqc_overrepresented_sequences_plot-1.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot-1.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot-1.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot-1.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot-1.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot-1.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", - "multiqc_citations.txt", - "multiqc_cutadapt.txt", "multiqc_data.json", "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", - "multiqc_fastqc_fastqc_raw.txt", - "multiqc_fastqc_fastqc_trimmed.txt", - "multiqc_featurecounts_biotype_plot.txt", "multiqc_general_stats.txt", "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", @@ -327,7 +297,6 @@ "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", - "multiqc_samtools_idxstats.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", @@ -339,16 +308,9 @@ "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", "picard_deduplication.txt", - "picard_histogram.txt", - "picard_histogram_1.txt", - "picard_histogram_2.txt", - "qualimap_gene_coverage_profile_Counts.txt", - "qualimap_gene_coverage_profile_Normalised.txt", "qualimap_genomic_origin.txt", - "qualimap_rnaseq_cov_hist.txt", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", - "rseqc_infer_experiment_plot.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", @@ -364,9 +326,6 @@ "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", "star_alignment_plot.txt", @@ -448,45 +407,21 @@ "png", "cutadapt_filtered_reads_plot-cnt.png", "cutadapt_filtered_reads_plot-pct.png", - "cutadapt_trimmed_sequences_plot_3_Counts.png", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "dupradar-section-plot.png", "fail_strand_check_table.png", - "fastqc-status-check-heatmap-1.png", - "fastqc-status-check-heatmap.png", "fastqc_adapter_content_plot.png", - "fastqc_overrepresented_sequences_plot-1.png", - "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot-1.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot-1.png", "fastqc_per_base_sequence_quality_plot.png", - "fastqc_per_sequence_gc_content_plot-1_Counts.png", - "fastqc_per_sequence_gc_content_plot-1_Percentages.png", - "fastqc_per_sequence_gc_content_plot_Counts.png", - "fastqc_per_sequence_gc_content_plot_Percentages.png", - "fastqc_per_sequence_quality_scores_plot-1.png", - "fastqc_per_sequence_quality_scores_plot.png", - "fastqc_sequence_counts_plot-1-cnt.png", - "fastqc_sequence_counts_plot-1-pct.png", - "fastqc_sequence_counts_plot-cnt.png", - "fastqc_sequence_counts_plot-pct.png", - "fastqc_sequence_duplication_levels_plot-1.png", - "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", - "featurecounts_biotype_plot-cnt.png", - "featurecounts_biotype_plot-pct.png", "general_stats_table.png", "picard_deduplication-cnt.png", "picard_deduplication-pct.png", - "qualimap_gene_coverage_profile_Counts.png", - "qualimap_gene_coverage_profile_Normalised.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", - "rseqc_infer_experiment_plot.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", @@ -498,18 +433,11 @@ "rseqc_junction_saturation_plot_Novel_Junctions.png", "rseqc_read_distribution_plot-cnt.png", "rseqc_read_distribution_plot-pct.png", - "rseqc_read_dups_plot.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png", "samtools-stats-dp.png", "samtools_alignment_plot-cnt.png", "samtools_alignment_plot-pct.png", @@ -596,86 +524,55 @@ "salmon", "RAP1_IAA_30M_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "deseq2_qc", - "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -699,19 +596,13 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", - "tx2gene.tsv", "star_salmon", "RAP1_IAA_30M_REP1", "RAP1_IAA_30M_REP1.markdup.sorted.bam", "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -722,13 +613,8 @@ "RAP1_UNINDUCED_REP1.markdup.sorted.bam", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -739,13 +625,8 @@ "RAP1_UNINDUCED_REP2.markdup.sorted.bam", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -756,13 +637,8 @@ "WT_REP1.markdup.sorted.bam", "WT_REP1.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -773,13 +649,8 @@ "WT_REP2.markdup.sorted.bam", "WT_REP2.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -798,7 +669,6 @@ "WT_REP2.forward.bigWig", "WT_REP2.reverse.bigWig", "deseq2_qc", - "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -818,11 +688,6 @@ "WT_REP1_duprateExpBoxplot.pdf", "WT_REP2_duprateExpBoxplot.pdf", "gene_data", - "RAP1_IAA_30M_REP1_dupMatrix.txt", - "RAP1_UNINDUCED_REP1_dupMatrix.txt", - "RAP1_UNINDUCED_REP2_dupMatrix.txt", - "WT_REP1_dupMatrix.txt", - "WT_REP2_dupMatrix.txt", "histogram", "RAP1_IAA_30M_REP1_expressionHist.pdf", "RAP1_UNINDUCED_REP1_expressionHist.pdf", @@ -830,11 +695,6 @@ "WT_REP1_expressionHist.pdf", "WT_REP2_expressionHist.pdf", "intercepts_slope", - "RAP1_IAA_30M_REP1_intercept_slope.txt", - "RAP1_UNINDUCED_REP1_intercept_slope.txt", - "RAP1_UNINDUCED_REP2_intercept_slope.txt", - "WT_REP1_intercept_slope.txt", - "WT_REP2_intercept_slope.txt", "scatter_plot", "RAP1_IAA_30M_REP1_duprateExpDens.pdf", "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", @@ -842,47 +702,27 @@ "WT_REP1_duprateExpDens.pdf", "WT_REP2_duprateExpDens.pdf", "featurecounts", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv", - "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv", - "RAP1_IAA_30M_REP1.featureCounts.txt", "RAP1_IAA_30M_REP1.featureCounts.txt.summary", - "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv", - "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv", - "RAP1_UNINDUCED_REP1.featureCounts.txt", "RAP1_UNINDUCED_REP1.featureCounts.txt.summary", - "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv", - "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv", - "RAP1_UNINDUCED_REP2.featureCounts.txt", "RAP1_UNINDUCED_REP2.featureCounts.txt.summary", - "WT_REP1.biotype_counts_mqc.tsv", - "WT_REP1.biotype_counts_rrna_mqc.tsv", - "WT_REP1.featureCounts.txt", "WT_REP1.featureCounts.txt.summary", - "WT_REP2.biotype_counts_mqc.tsv", - "WT_REP2.biotype_counts_rrna_mqc.tsv", - "WT_REP2.featureCounts.txt", "WT_REP2.featureCounts.txt.summary", "log", "RAP1_IAA_30M_REP1.Log.final.out", "RAP1_IAA_30M_REP1.Log.out", "RAP1_IAA_30M_REP1.Log.progress.out", - "RAP1_IAA_30M_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP1.Log.final.out", "RAP1_UNINDUCED_REP1.Log.out", "RAP1_UNINDUCED_REP1.Log.progress.out", - "RAP1_UNINDUCED_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP2.Log.final.out", "RAP1_UNINDUCED_REP2.Log.out", "RAP1_UNINDUCED_REP2.Log.progress.out", - "RAP1_UNINDUCED_REP2.SJ.out.tab", "WT_REP1.Log.final.out", "WT_REP1.Log.out", "WT_REP1.Log.progress.out", - "WT_REP1.SJ.out.tab", "WT_REP2.Log.final.out", "WT_REP2.Log.out", "WT_REP2.Log.progress.out", - "WT_REP2.SJ.out.tab", "picard_metrics", "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -895,190 +735,90 @@ "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "rseqc", "bam_stat", @@ -1088,11 +828,6 @@ "WT_REP1.bam_stat.txt", "WT_REP2.bam_stat.txt", "infer_experiment", - "RAP1_IAA_30M_REP1.infer_experiment.txt", - "RAP1_UNINDUCED_REP1.infer_experiment.txt", - "RAP1_UNINDUCED_REP2.infer_experiment.txt", - "WT_REP1.infer_experiment.txt", - "WT_REP2.infer_experiment.txt", "inner_distance", "pdf", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", @@ -1241,51 +976,30 @@ "WT_REP2.sorted.bam.stats", "stringtie", "RAP1_IAA_30M_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_IAA_30M_REP1.coverage.gtf", "RAP1_IAA_30M_REP1.gene.abundance.txt", "RAP1_IAA_30M_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP1.coverage.gtf", "RAP1_UNINDUCED_REP1.gene.abundance.txt", "RAP1_UNINDUCED_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP2.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP2.coverage.gtf", "RAP1_UNINDUCED_REP2.gene.abundance.txt", "RAP1_UNINDUCED_REP2.transcripts.gtf", "WT_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "WT_REP1.coverage.gtf", "WT_REP1.gene.abundance.txt", "WT_REP1.transcripts.gtf", "WT_REP2.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "WT_REP2.coverage.gtf", "WT_REP2.gene.abundance.txt", "WT_REP2.transcripts.gtf", - "tx2gene.tsv", "trimgalore", "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", @@ -1589,6 +1303,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T15:24:24.41718" + "timestamp": "2024-09-17T18:29:56.535818" } } \ No newline at end of file diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 3bde9696b..1c9e6ae59 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -13,15 +13,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } @@ -39,15 +40,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 910c241bc..a1c47f5c0 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -1,6 +1,7 @@ { "Params: --aligner hisat2 - stub": { "content": [ + 23, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -43,14 +44,12 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.1" + "nf-core/rnaseq": "v3.16.0dev" } }, [ "custom", "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw.html", @@ -82,17 +81,19 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ - + "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T12:55:56.074105" + "timestamp": "2024-09-17T18:45:38.656164" }, "Params: --aligner hisat2": { "content": [ + 187, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -221,7 +222,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.1" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -233,8 +234,6 @@ "WT_REP2.stats.txt", "custom", "out", - "genome_gfp.fasta", - "genome_gfp.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw_1_fastqc.html", @@ -300,11 +299,6 @@ "WT_REP1_duprateExpBoxplot.pdf", "WT_REP2_duprateExpBoxplot.pdf", "gene_data", - "RAP1_IAA_30M_REP1_dupMatrix.txt", - "RAP1_UNINDUCED_REP1_dupMatrix.txt", - "RAP1_UNINDUCED_REP2_dupMatrix.txt", - "WT_REP1_dupMatrix.txt", - "WT_REP2_dupMatrix.txt", "histogram", "RAP1_IAA_30M_REP1_expressionHist.pdf", "RAP1_UNINDUCED_REP1_expressionHist.pdf", @@ -312,11 +306,6 @@ "WT_REP1_expressionHist.pdf", "WT_REP2_expressionHist.pdf", "intercepts_slope", - "RAP1_IAA_30M_REP1_intercept_slope.txt", - "RAP1_UNINDUCED_REP1_intercept_slope.txt", - "RAP1_UNINDUCED_REP2_intercept_slope.txt", - "WT_REP1_intercept_slope.txt", - "WT_REP2_intercept_slope.txt", "scatter_plot", "RAP1_IAA_30M_REP1_duprateExpDens.pdf", "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", @@ -324,32 +313,12 @@ "WT_REP1_duprateExpDens.pdf", "WT_REP2_duprateExpDens.pdf", "featurecounts", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv", - "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv", - "RAP1_IAA_30M_REP1.featureCounts.txt", "RAP1_IAA_30M_REP1.featureCounts.txt.summary", - "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv", - "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv", - "RAP1_UNINDUCED_REP1.featureCounts.txt", "RAP1_UNINDUCED_REP1.featureCounts.txt.summary", - "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv", - "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv", - "RAP1_UNINDUCED_REP2.featureCounts.txt", "RAP1_UNINDUCED_REP2.featureCounts.txt.summary", - "WT_REP1.biotype_counts_mqc.tsv", - "WT_REP1.biotype_counts_rrna_mqc.tsv", - "WT_REP1.featureCounts.txt", "WT_REP1.featureCounts.txt.summary", - "WT_REP2.biotype_counts_mqc.tsv", - "WT_REP2.biotype_counts_rrna_mqc.tsv", - "WT_REP2.featureCounts.txt", "WT_REP2.featureCounts.txt.summary", "log", - "RAP1_IAA_30M_REP1.hisat2.summary.log", - "RAP1_UNINDUCED_REP1.hisat2.summary.log", - "RAP1_UNINDUCED_REP2.hisat2.summary.log", - "WT_REP1.hisat2.summary.log", - "WT_REP2.hisat2.summary.log", "picard_metrics", "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -362,190 +331,90 @@ "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "rseqc", "bam_stat", @@ -555,11 +424,6 @@ "WT_REP1.bam_stat.txt", "WT_REP2.bam_stat.txt", "infer_experiment", - "RAP1_IAA_30M_REP1.infer_experiment.txt", - "RAP1_UNINDUCED_REP1.infer_experiment.txt", - "RAP1_UNINDUCED_REP2.infer_experiment.txt", - "WT_REP1.infer_experiment.txt", - "WT_REP2.infer_experiment.txt", "inner_distance", "pdf", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", @@ -696,46 +560,26 @@ "WT_REP2.sorted.bam.stats", "stringtie", "RAP1_IAA_30M_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_IAA_30M_REP1.coverage.gtf", "RAP1_IAA_30M_REP1.gene.abundance.txt", "RAP1_IAA_30M_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP1.coverage.gtf", "RAP1_UNINDUCED_REP1.gene.abundance.txt", "RAP1_UNINDUCED_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP2.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP2.coverage.gtf", "RAP1_UNINDUCED_REP2.gene.abundance.txt", "RAP1_UNINDUCED_REP2.transcripts.gtf", "WT_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "WT_REP1.coverage.gtf", "WT_REP1.gene.abundance.txt", "WT_REP1.transcripts.gtf", "WT_REP2.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "WT_REP2.coverage.gtf", "WT_REP2.gene.abundance.txt", @@ -744,43 +588,14 @@ "hisat2", "multiqc_report.html", "multiqc_report_data", - "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "fastqc-status-check-heatmap-1.txt", - "fastqc-status-check-heatmap.txt", - "fastqc_adapter_content_plot.txt", - "fastqc_overrepresented_sequences_plot-1.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot-1.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot-1.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot-1.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot-1.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot-1.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "hisat2_pe_plot.txt", - "hisat2_se_plot.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", - "multiqc_citations.txt", - "multiqc_cutadapt.txt", "multiqc_data.json", "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", - "multiqc_fastqc_fastqc_raw.txt", - "multiqc_fastqc_fastqc_trimmed.txt", - "multiqc_featurecounts_biotype_plot.txt", "multiqc_general_stats.txt", "multiqc_hisat2.txt", "multiqc_picard_dups.txt", @@ -796,21 +611,13 @@ "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", - "multiqc_samtools_idxstats.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", "picard_deduplication.txt", - "picard_histogram.txt", - "picard_histogram_1.txt", - "picard_histogram_2.txt", - "qualimap_gene_coverage_profile_Counts.txt", - "qualimap_gene_coverage_profile_Normalised.txt", "qualimap_genomic_origin.txt", - "qualimap_rnaseq_cov_hist.txt", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", - "rseqc_infer_experiment_plot.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", @@ -826,9 +633,6 @@ "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", "multiqc_report_plots", @@ -866,10 +670,6 @@ "featurecounts_biotype_plot-cnt.pdf", "featurecounts_biotype_plot-pct.pdf", "general_stats_table.pdf", - "hisat2_pe_plot-cnt.pdf", - "hisat2_pe_plot-pct.pdf", - "hisat2_se_plot-cnt.pdf", - "hisat2_se_plot-pct.pdf", "picard_deduplication-cnt.pdf", "picard_deduplication-pct.pdf", "qualimap_gene_coverage_profile_Counts.pdf", @@ -907,49 +707,21 @@ "png", "cutadapt_filtered_reads_plot-cnt.png", "cutadapt_filtered_reads_plot-pct.png", - "cutadapt_trimmed_sequences_plot_3_Counts.png", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "dupradar-section-plot.png", "fail_strand_check_table.png", - "fastqc-status-check-heatmap-1.png", - "fastqc-status-check-heatmap.png", "fastqc_adapter_content_plot.png", - "fastqc_overrepresented_sequences_plot-1.png", - "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot-1.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot-1.png", "fastqc_per_base_sequence_quality_plot.png", - "fastqc_per_sequence_gc_content_plot-1_Counts.png", - "fastqc_per_sequence_gc_content_plot-1_Percentages.png", - "fastqc_per_sequence_gc_content_plot_Counts.png", - "fastqc_per_sequence_gc_content_plot_Percentages.png", - "fastqc_per_sequence_quality_scores_plot-1.png", - "fastqc_per_sequence_quality_scores_plot.png", - "fastqc_sequence_counts_plot-1-cnt.png", - "fastqc_sequence_counts_plot-1-pct.png", - "fastqc_sequence_counts_plot-cnt.png", - "fastqc_sequence_counts_plot-pct.png", - "fastqc_sequence_duplication_levels_plot-1.png", - "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", - "featurecounts_biotype_plot-cnt.png", - "featurecounts_biotype_plot-pct.png", "general_stats_table.png", - "hisat2_pe_plot-cnt.png", - "hisat2_pe_plot-pct.png", - "hisat2_se_plot-cnt.png", - "hisat2_se_plot-pct.png", "picard_deduplication-cnt.png", "picard_deduplication-pct.png", - "qualimap_gene_coverage_profile_Counts.png", - "qualimap_gene_coverage_profile_Normalised.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", - "rseqc_infer_experiment_plot.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", @@ -961,18 +733,11 @@ "rseqc_junction_saturation_plot_Novel_Junctions.png", "rseqc_read_distribution_plot-cnt.png", "rseqc_read_distribution_plot-pct.png", - "rseqc_read_dups_plot.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png", "samtools-stats-dp.png", "samtools_alignment_plot-cnt.png", "samtools_alignment_plot-pct.png", @@ -1010,10 +775,6 @@ "featurecounts_biotype_plot-cnt.svg", "featurecounts_biotype_plot-pct.svg", "general_stats_table.svg", - "hisat2_pe_plot-cnt.svg", - "hisat2_pe_plot-pct.svg", - "hisat2_se_plot-cnt.svg", - "hisat2_se_plot-pct.svg", "picard_deduplication-cnt.svg", "picard_deduplication-pct.svg", "qualimap_gene_coverage_profile_Counts.svg", @@ -1053,86 +814,55 @@ "salmon", "RAP1_IAA_30M_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "deseq2_qc", - "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -1156,7 +886,6 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", - "tx2gene.tsv", "trimgalore", "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", @@ -1168,6 +897,8 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ + "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", + "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,8a6bf324a928534cb7ed7a5522aff7d0", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,ae3e70edc98ec8117608f8f608effab9", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,9a5c2672c5817e930c7b884ada8fd92c", @@ -1193,18 +924,108 @@ "WT_REP2.biotype_counts_mqc.tsv:md5,74a5436a716a7d99f425f73914cb2794", 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"comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + "comment.png:md5,882e40f3d6a16c6ed35659b105251525", + "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", + "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", + "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", + "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", + "Coverage Profile Along Genes (High).png:md5,f63458b8564de80c90c992926ea273ed", + "Coverage Profile Along Genes (Low).png:md5,44f0dd7c647a2ce2c1f06e3920266e95", + "Coverage Profile Along Genes (Total).png:md5,12780d9ad7b76dbdd39736099c45cf07", + "Transcript coverage histogram.png:md5,fcc848c9d318a28c7dff00cb2960e038", "coverage_profile_along_genes_(high).txt:md5,83d436e0ddb7435bb343db5e4dfb744a", "coverage_profile_along_genes_(low).txt:md5,58021e91f3595a0d6dc74abc41690638", "coverage_profile_along_genes_(total).txt:md5,58021e91f3595a0d6dc74abc41690638", @@ -1213,6 +1034,26 @@ "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,3d17628d178e5a3cc9dc03f32614bff7", "WT_REP1.infer_experiment.txt:md5,13e3c748f5b968455a39eb9fefd87053", "WT_REP2.infer_experiment.txt:md5,230910b354a5531d1c4bf711ccd6e493", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,c93ce5b90352398208e3d88c68df45c6", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,fe9d92d1d28e1bc1b223e2ce22b4ef05", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,293d64f70bd8353b822e4fa8a6f082a3", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,d279003d92f7feef9adb31203f84474a", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,ed48a29b77c315cb61a6bf09e68c877d", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,cf2506824949c02e0bfde17a9ed86e61", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,a17c7749a005a89875876eb2d90721d4", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,2e2d760739539fba09cbb666ab95afa1", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,22bdc84c1c4acce9798868e8c7b56004", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,80fe14762a8f7230d516bba37b7275d1", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -1253,21 +1094,80 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3625f666cc09d0f07990716aeccd869f", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,6c323b383a6506d124506405b9463d93", + "hisat2_pe_plot-cnt.pdf:md5,5ea21b11336a653206216b189619615d", + "hisat2_pe_plot-pct.pdf:md5,97920acd4cd0ef6c347d1e5196378316", + "hisat2_se_plot-cnt.pdf:md5,162ad273b806726ee519dd85a0ee5521", + "hisat2_se_plot-pct.pdf:md5,6fad42a1c9973d5315bfa6895ef0b8a0", + "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", + "dupradar-section-plot.png:md5,6074ea2315d296094bd10fad3dcc475b", + "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890", + "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84", + "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f", + "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14", + "fastqc_per_sequence_gc_content_plot-1_Counts.png:md5,8a806cec2142f9911502e0a253d83d13", + "fastqc_per_sequence_gc_content_plot-1_Percentages.png:md5,953929d50c8490029880e205e4db7959", + "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16", + "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,eba3abf8bedb2cb20bad90c54e9c8881", + "fastqc_per_sequence_quality_scores_plot-1.png:md5,d2c29cae169f35744500c751b4a7366e", + "fastqc_per_sequence_quality_scores_plot.png:md5,42fd7369a8aca78f620164a9e887c3cb", + "fastqc_sequence_counts_plot-1-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", + "fastqc_sequence_counts_plot-1-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", + "fastqc_sequence_counts_plot-cnt.png:md5,3890d5555f2a39b46b9f6efb14cb91f2", + "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054", + "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", + "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", + "featurecounts_biotype_plot-cnt.png:md5,138e00d2fe0af27f2979cf7bdff83b46", + "featurecounts_biotype_plot-pct.png:md5,3b7550efe9068f3ada2cc64e311f3338", + "hisat2_pe_plot-cnt.png:md5,1e0841cb32f6aaad84772ff2267b70ad", + "hisat2_pe_plot-pct.png:md5,e201931cd7b31e7227a6273ca1587f56", + "hisat2_se_plot-cnt.png:md5,840937eb5952fa98987a1d2aa8267959", + "hisat2_se_plot-pct.png:md5,51bb5f9ba36dab1ba32fc4e273e865a9", + "qualimap_gene_coverage_profile_Counts.png:md5,1aa39028b017760d0b09f1b6f8c1fa3a", + "qualimap_gene_coverage_profile_Normalised.png:md5,1cd382a79b89564a006afe431aa3916d", + "rseqc_infer_experiment_plot.png:md5,73f5b860029912da9c3f6a887238d251", + "rseqc_read_dups_plot.png:md5,fbb8a2268f0468be5a94c960bd2ebd2a", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,a56226e705754ce81c7709d40794dd92", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,3bb99f72a15a4159860008beea8c802b", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,25015f9be4710c4eccc50f30db3bf521", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,baa90f5ad4d999fc60db30840b72d8c6", + "hisat2_pe_plot-cnt.svg:md5,dae72c87e9e5892ebc1ed5937b737d66", + "hisat2_pe_plot-pct.svg:md5,37d72b7dfc24210dd4f8322f2bb7c801", + "hisat2_se_plot-cnt.svg:md5,785d8da961280cfcd6562bb8b1f8b682", + "hisat2_se_plot-pct.svg:md5,ae694bcf0d5019a534517583507aaaa9", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", + "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], @@ -1275,6 +1175,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T12:54:59.807236" + "timestamp": "2024-09-17T18:44:49.645101" } } \ No newline at end of file diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index 0d8f63e93..f81070439 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -15,15 +15,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } @@ -43,15 +44,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index bbdf72a9b..c09795a73 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -1,6 +1,7 @@ { "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment": { "content": [ + 35, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -55,7 +56,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.1" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -67,8 +68,6 @@ "WT_REP2.stats.txt", "custom", "out", - "genome_gfp.fasta", - "genome_gfp.gtf", "fastqc", "trim", "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", @@ -90,28 +89,18 @@ "kallisto", "RAP1_IAA_30M_REP1", "abundance.h5", - "abundance.tsv", - "kallisto_quant.log", "run_info.json", "RAP1_UNINDUCED_REP1", "abundance.h5", - "abundance.tsv", - "kallisto_quant.log", "run_info.json", "RAP1_UNINDUCED_REP2", "abundance.h5", - "abundance.tsv", - "kallisto_quant.log", "run_info.json", "WT_REP1", "abundance.h5", - "abundance.tsv", - "kallisto_quant.log", "run_info.json", "WT_REP2", "abundance.h5", - "abundance.tsv", - "kallisto_quant.log", "run_info.json", "kallisto.merged.gene_counts.SummarizedExperiment.rds", "kallisto.merged.gene_counts.tsv", @@ -125,29 +114,12 @@ "kallisto.merged.transcript_counts.tsv", "kallisto.merged.transcript_lengths.tsv", "kallisto.merged.transcript_tpm.tsv", - "tx2gene.tsv", "multiqc", "multiqc_report.html", "multiqc_report_data", - "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "fastqc-status-check-heatmap.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table.txt", "kallisto_alignment.txt", - "multiqc_citations.txt", - "multiqc_cutadapt.txt", "multiqc_data.json", - "multiqc_fastqc_fastqc_trimmed.txt", "multiqc_general_stats.txt", "multiqc_kallisto.txt", "multiqc_software_versions.txt", @@ -171,28 +143,14 @@ "fastqc_sequence_length_distribution_plot.pdf", "fastqc_top_overrepresented_sequences_table.pdf", "general_stats_table.pdf", - "kallisto_alignment-cnt.pdf", - "kallisto_alignment-pct.pdf", "png", "cutadapt_filtered_reads_plot-cnt.png", "cutadapt_filtered_reads_plot-pct.png", - "cutadapt_trimmed_sequences_plot_3_Counts.png", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "fastqc-status-check-heatmap.png", - "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot.png", - "fastqc_per_sequence_gc_content_plot_Counts.png", - "fastqc_per_sequence_gc_content_plot_Percentages.png", - "fastqc_per_sequence_quality_scores_plot.png", - "fastqc_sequence_counts_plot-cnt.png", - "fastqc_sequence_counts_plot-pct.png", - "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", - "kallisto_alignment-cnt.png", - "kallisto_alignment-pct.png", "svg", "cutadapt_filtered_reads_plot-cnt.svg", "cutadapt_filtered_reads_plot-pct.svg", @@ -211,8 +169,6 @@ "fastqc_sequence_length_distribution_plot.svg", "fastqc_top_overrepresented_sequences_table.svg", "general_stats_table.svg", - "kallisto_alignment-cnt.svg", - "kallisto_alignment-pct.svg", "pipeline_info", "nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", @@ -226,11 +182,18 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ + "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", + "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", "abundance.tsv:md5,b6ae4ef44f718a789f58dc6451b6eebb", + "kallisto_quant.log:md5,88a4a4c71762af549f1c42308fe80605", "abundance.tsv:md5,a2c6108c384662f4da8c7b7fe8f27e02", + "kallisto_quant.log:md5,b9c4528ce7c00f5f94e7570507d00a51", "abundance.tsv:md5,6fd77021287360f5005c90807233ab23", + "kallisto_quant.log:md5,8a9605e9d228c9cbec97b0883d909754", "abundance.tsv:md5,7b62c5df0930e9f5ebc6e90d6aa600f6", + "kallisto_quant.log:md5,5a7f563172800853c627e8e4f5da6bdc", "abundance.tsv:md5,6fb211dc8e4fd238ca68d21d6cc83cf5", + "kallisto_quant.log:md5,3447f945ddb20a8eca8aef31b088b8d5", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", @@ -247,17 +210,34 @@ "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804" + "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", + "kallisto_alignment-cnt.pdf:md5,a2aa89be43ff1264be51860419219648", + "kallisto_alignment-pct.pdf:md5,41ac1dcf4b41baa598368783eadd92ab", + "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", + "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890", + "fastqc_overrepresented_sequences_plot.png:md5,40e450251b80ec0efc9364434234ec7f", + "fastqc_per_sequence_gc_content_plot_Counts.png:md5,8a806cec2142f9911502e0a253d83d13", + "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,953929d50c8490029880e205e4db7959", + "fastqc_per_sequence_quality_scores_plot.png:md5,d2c29cae169f35744500c751b4a7366e", + "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", + "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", + "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", + "kallisto_alignment-cnt.png:md5,989083624e0905b82cbca32f7001a225", + "kallisto_alignment-pct.png:md5,f4de4c6c0fa3ccc83deca870ea2448d2", + "kallisto_alignment-cnt.svg:md5,fc7978ac83c82a3fcc58bb981471a1ee", + "kallisto_alignment-pct.svg:md5,bba0ff4f756a99d943b5b7fff4ab668e" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T12:59:06.669773" + "timestamp": "2024-09-17T18:49:01.323612" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ + 17, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -294,14 +274,12 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.1" + "nf-core/rnaseq": "v3.16.0dev" } }, [ "custom", "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", "fastqc", "trim", "multiqc", @@ -321,13 +299,14 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ - + "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T12:59:50.009267" + "timestamp": "2024-09-17T18:49:45.661258" } } \ No newline at end of file diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index 4ff001eb4..a6b5c512d 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -10,26 +10,35 @@ class UTILS { public static getAllFilesFromDir(dir, List includeRegexes = null, List excludeRegexes = null) { def output = [] new File(dir).eachFileRecurse() { file -> - boolean matchesInclusion = (includeRegexes == null || includeRegexes.any { regex -> file.name.toString() ==~ regex }) - boolean matchesExclusion = (excludeRegexes == null || !excludeRegexes.any { regex -> file.name.toString() ==~ regex }) - - // Conditionally add either file path or just the file name - if (matchesInclusion && matchesExclusion) output.add(file) + boolean matchesInclusion = includeRegexes ? includeRegexes.any { regex -> file.name.toString() ==~ regex } : true + boolean matchesExclusion = excludeRegexes ? excludeRegexes.any { regex -> file.name.toString() ==~ regex } : false + // Add files to the list if they match the includeRegexes and not the excludeRegexes + if (matchesInclusion && !matchesExclusion) output.add(file) } return output.sort { it.path } } - // Static (global) exclusion regexes list static List exclusionRegexesForUnstableFileNames = [/.*\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}.*/] - static List snapshottablePatterns = [/.*\.(ctab|fasta|gtf|gz|json|log|png|tab|tsv|txt)$/] + + // These are the extension of all files to try to snapshot + static List snapshottablePatterns = [/.*\.(ctab|fasta|gtf|gz|html|json|log|pdf|png|svg|tab|tsv|txt|yml)$/] + + // These are the files to exclude when we want to snapshot static List exclusionRegexesForUnstableFileContents = [ // To exclude files with timestamps in the format YYYY-MM-DD_HH-MM-SS - /\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}/, + /.*\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}.*/, + + // To exlude the pipeline_software_mqc_versions.yml file that contains the Nextflow version + /nf_core_rnaseq_software_mqc_versions\.yml/, // To exlude bbsplit files /.*\.stats\.txt/, + // To exclude FASTQC reports + /.*_raw\.html/, + /.*_fastqc\.html/, + // To exclude from the MultiQC reports /cutadapt_filtered_reads_plot-.*/, /cutadapt_trimmed_sequences_.*\.pdf/, diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index c1622036f..7da136cdd 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -13,15 +13,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } @@ -39,15 +40,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index a112fcca2..49e7fad77 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -1,6 +1,7 @@ { "Params: --min_mapped_reads 90": { "content": [ + 152, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -133,7 +134,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.1" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -145,8 +146,6 @@ "WT_REP2.stats.txt", "custom", "out", - "genome_gfp.fasta", - "genome_gfp.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw_1_fastqc.html", @@ -186,42 +185,13 @@ "star_salmon", "multiqc_report.html", "multiqc_report_data", - "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "fastqc-status-check-heatmap-1.txt", - "fastqc-status-check-heatmap.txt", - "fastqc_adapter_content_plot.txt", - "fastqc_overrepresented_sequences_plot-1.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot-1.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot-1.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot-1.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot-1.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot-1.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", - "multiqc_citations.txt", - "multiqc_cutadapt.txt", "multiqc_data.json", "multiqc_dupradar-section-plot.txt", - "multiqc_fail_mapped_samples_table.txt", "multiqc_fail_strand_check_table.txt", - "multiqc_fastqc_fastqc_raw.txt", - "multiqc_fastqc_fastqc_trimmed.txt", - "multiqc_featurecounts_biotype_plot.txt", "multiqc_general_stats.txt", "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", @@ -236,7 +206,6 @@ "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", - "multiqc_samtools_idxstats.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", @@ -248,16 +217,9 @@ "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", "picard_deduplication.txt", - "picard_histogram.txt", - "picard_histogram_1.txt", - "picard_histogram_2.txt", - "qualimap_gene_coverage_profile_Counts.txt", - "qualimap_gene_coverage_profile_Normalised.txt", "qualimap_genomic_origin.txt", - "qualimap_rnaseq_cov_hist.txt", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", - "rseqc_infer_experiment_plot.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", @@ -273,9 +235,6 @@ "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", "star_alignment_plot.txt", @@ -287,7 +246,6 @@ "cutadapt_trimmed_sequences_plot_3_Counts.pdf", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", "dupradar-section-plot.pdf", - "fail_mapped_samples_table.pdf", "fail_strand_check_table.pdf", "fastqc-status-check-heatmap-1.pdf", "fastqc-status-check-heatmap.pdf", @@ -358,46 +316,21 @@ "png", "cutadapt_filtered_reads_plot-cnt.png", "cutadapt_filtered_reads_plot-pct.png", - "cutadapt_trimmed_sequences_plot_3_Counts.png", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "dupradar-section-plot.png", - "fail_mapped_samples_table.png", "fail_strand_check_table.png", - "fastqc-status-check-heatmap-1.png", - "fastqc-status-check-heatmap.png", "fastqc_adapter_content_plot.png", - "fastqc_overrepresented_sequences_plot-1.png", - "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot-1.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot-1.png", "fastqc_per_base_sequence_quality_plot.png", - "fastqc_per_sequence_gc_content_plot-1_Counts.png", - "fastqc_per_sequence_gc_content_plot-1_Percentages.png", - "fastqc_per_sequence_gc_content_plot_Counts.png", - "fastqc_per_sequence_gc_content_plot_Percentages.png", - "fastqc_per_sequence_quality_scores_plot-1.png", - "fastqc_per_sequence_quality_scores_plot.png", - "fastqc_sequence_counts_plot-1-cnt.png", - "fastqc_sequence_counts_plot-1-pct.png", - "fastqc_sequence_counts_plot-cnt.png", - "fastqc_sequence_counts_plot-pct.png", - "fastqc_sequence_duplication_levels_plot-1.png", - "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", - "featurecounts_biotype_plot-cnt.png", - "featurecounts_biotype_plot-pct.png", "general_stats_table.png", "picard_deduplication-cnt.png", "picard_deduplication-pct.png", - "qualimap_gene_coverage_profile_Counts.png", - "qualimap_gene_coverage_profile_Normalised.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", - "rseqc_infer_experiment_plot.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", @@ -409,18 +342,11 @@ "rseqc_junction_saturation_plot_Novel_Junctions.png", "rseqc_read_distribution_plot-cnt.png", "rseqc_read_distribution_plot-pct.png", - "rseqc_read_dups_plot.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png", "samtools-stats-dp.png", "samtools_alignment_plot-cnt.png", "samtools_alignment_plot-pct.png", @@ -435,7 +361,6 @@ "cutadapt_trimmed_sequences_plot_3_Counts.svg", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", "dupradar-section-plot.svg", - "fail_mapped_samples_table.svg", "fail_strand_check_table.svg", "fastqc-status-check-heatmap-1.svg", "fastqc-status-check-heatmap.svg", @@ -508,86 +433,55 @@ "salmon", "RAP1_IAA_30M_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "deseq2_qc", - "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -611,19 +505,13 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", - "tx2gene.tsv", "star_salmon", "RAP1_IAA_30M_REP1", "RAP1_IAA_30M_REP1.markdup.sorted.bam", "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -634,13 +522,8 @@ "RAP1_UNINDUCED_REP1.markdup.sorted.bam", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -651,13 +534,8 @@ "RAP1_UNINDUCED_REP2.markdup.sorted.bam", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -666,13 +544,8 @@ "quant.sf", "WT_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -681,13 +554,8 @@ "quant.sf", "WT_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -702,7 +570,6 @@ "RAP1_UNINDUCED_REP2.forward.bigWig", "RAP1_UNINDUCED_REP2.reverse.bigWig", "deseq2_qc", - "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -720,55 +587,35 @@ "RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf", "RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf", "gene_data", - "RAP1_IAA_30M_REP1_dupMatrix.txt", - "RAP1_UNINDUCED_REP1_dupMatrix.txt", - "RAP1_UNINDUCED_REP2_dupMatrix.txt", "histogram", "RAP1_IAA_30M_REP1_expressionHist.pdf", "RAP1_UNINDUCED_REP1_expressionHist.pdf", "RAP1_UNINDUCED_REP2_expressionHist.pdf", "intercepts_slope", - "RAP1_IAA_30M_REP1_intercept_slope.txt", - "RAP1_UNINDUCED_REP1_intercept_slope.txt", - "RAP1_UNINDUCED_REP2_intercept_slope.txt", "scatter_plot", "RAP1_IAA_30M_REP1_duprateExpDens.pdf", "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", "RAP1_UNINDUCED_REP2_duprateExpDens.pdf", "featurecounts", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv", - "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv", - "RAP1_IAA_30M_REP1.featureCounts.txt", "RAP1_IAA_30M_REP1.featureCounts.txt.summary", - "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv", - "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv", - "RAP1_UNINDUCED_REP1.featureCounts.txt", "RAP1_UNINDUCED_REP1.featureCounts.txt.summary", - "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv", - "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv", - "RAP1_UNINDUCED_REP2.featureCounts.txt", "RAP1_UNINDUCED_REP2.featureCounts.txt.summary", "log", "RAP1_IAA_30M_REP1.Log.final.out", "RAP1_IAA_30M_REP1.Log.out", "RAP1_IAA_30M_REP1.Log.progress.out", - "RAP1_IAA_30M_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP1.Log.final.out", "RAP1_UNINDUCED_REP1.Log.out", "RAP1_UNINDUCED_REP1.Log.progress.out", - "RAP1_UNINDUCED_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP2.Log.final.out", "RAP1_UNINDUCED_REP2.Log.out", "RAP1_UNINDUCED_REP2.Log.progress.out", - "RAP1_UNINDUCED_REP2.SJ.out.tab", "WT_REP1.Log.final.out", "WT_REP1.Log.out", "WT_REP1.Log.progress.out", - "WT_REP1.SJ.out.tab", "WT_REP2.Log.final.out", "WT_REP2.Log.out", "WT_REP2.Log.progress.out", - "WT_REP2.SJ.out.tab", "picard_metrics", "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -779,114 +626,54 @@ "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "rseqc", "bam_stat", @@ -894,9 +681,6 @@ "RAP1_UNINDUCED_REP1.bam_stat.txt", "RAP1_UNINDUCED_REP2.bam_stat.txt", "infer_experiment", - "RAP1_IAA_30M_REP1.infer_experiment.txt", - "RAP1_UNINDUCED_REP1.infer_experiment.txt", - "RAP1_UNINDUCED_REP2.infer_experiment.txt", "inner_distance", "pdf", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", @@ -1001,33 +785,20 @@ "WT_REP2.sorted.bam.stats", "stringtie", "RAP1_IAA_30M_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_IAA_30M_REP1.coverage.gtf", "RAP1_IAA_30M_REP1.gene.abundance.txt", "RAP1_IAA_30M_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP1.coverage.gtf", "RAP1_UNINDUCED_REP1.gene.abundance.txt", "RAP1_UNINDUCED_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP2.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP2.coverage.gtf", "RAP1_UNINDUCED_REP2.gene.abundance.txt", "RAP1_UNINDUCED_REP2.transcripts.gtf", - "tx2gene.tsv", "trimgalore", "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", @@ -1039,6 +810,8 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ + "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", + "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -1079,32 +852,98 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "fail_mapped_samples_table.pdf:md5,0d7f9889a09b43eb633b643fd2607442", + "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", + "dupradar-section-plot.png:md5,eacbc664cc29a7a59a6aa366b4618582", + "fail_mapped_samples_table.png:md5,e0702273ab75b55895e566cb2945d893", + "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890", + "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84", + "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f", + "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14", + "fastqc_per_sequence_gc_content_plot-1_Counts.png:md5,8a806cec2142f9911502e0a253d83d13", + "fastqc_per_sequence_gc_content_plot-1_Percentages.png:md5,953929d50c8490029880e205e4db7959", + "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16", + "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,eba3abf8bedb2cb20bad90c54e9c8881", + "fastqc_per_sequence_quality_scores_plot-1.png:md5,d2c29cae169f35744500c751b4a7366e", + "fastqc_per_sequence_quality_scores_plot.png:md5,42fd7369a8aca78f620164a9e887c3cb", + "fastqc_sequence_counts_plot-1-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", + "fastqc_sequence_counts_plot-1-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", + "fastqc_sequence_counts_plot-cnt.png:md5,3890d5555f2a39b46b9f6efb14cb91f2", + "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054", + "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", + "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", + "featurecounts_biotype_plot-cnt.png:md5,95b10627fff1af0a209b8e380f4a4d0b", + "featurecounts_biotype_plot-pct.png:md5,f9c1cf03824ff9ba7da8537ecd93945b", + "qualimap_gene_coverage_profile_Counts.png:md5,2d54a60bef3dfa978da48c1b6872c41c", + "qualimap_gene_coverage_profile_Normalised.png:md5,a85a901be4c08c9dfcfd9fc87d890c1e", + "rseqc_infer_experiment_plot.png:md5,5ce01a7b923f4e6433b76dd88ca22f42", + "rseqc_read_dups_plot.png:md5,bdc7281c52b54a5784aa0d714f9c255e", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,d5d8a85b7ad72a0cb93d9283ea12b23f", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,a6849cd92ae738441212b681a411614d", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f", + "fail_mapped_samples_table.svg:md5,e98423866a8f26e67866e81342862256", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + 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"ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", @@ -1120,18 +959,86 @@ "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,b621ce1e803d8670ece6c66391c33ba4", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,480b2586a878bc22f5b73f94051b41d8", + "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", + "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", + "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", + "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204", + "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", + "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + "comment.png:md5,882e40f3d6a16c6ed35659b105251525", + "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", + "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", + "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", + "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", + "Coverage Profile Along Genes (High).png:md5,876c1b88f33bd3e5fe1a41679729573d", + "Coverage Profile Along Genes (Low).png:md5,ee1f2c9cc4dd4867811eda1e68864ab4", + "Coverage Profile Along Genes (Total).png:md5,53747a8f9813744902756ad60638380a", + "Transcript coverage histogram.png:md5,4f9072d4b11216373b59396293803a37", "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8", "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", + "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + 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"coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", + "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + "comment.png:md5,882e40f3d6a16c6ed35659b105251525", + "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", + "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", + "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", + "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", + "Coverage Profile Along Genes (High).png:md5,5a5d99cc7a1dba3762d67f4aa4adad58", + "Coverage Profile Along Genes (Low).png:md5,b6adc296e9a732aa0495a6da8fa4ed90", + "Coverage Profile Along Genes (Total).png:md5,fcb94fb9c1a51c1db32f884d05929cc8", + "Transcript coverage histogram.png:md5,3aeb52ff3e3752727a370b0d7ceb0518", "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d", "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d", "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,169d25b95c008bebe9ce886fea6a4e33", "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,2ca0ce0fd3204bd2cc4812c4655b1f1f", "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,7d5705880188f9beab1939e08d6b8f40", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,3f149502efe2a9d4bac98b1dd18c15e7", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,a052ab04070e72cc318fb7680b0764e3", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,e82329a443b9ff50a86e42aff91bd704", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,d279003d92f7feef9adb31203f84474a", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,10e2d00f93f9e74f224bd3c1bfbeb29b", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], @@ -1139,10 +1046,11 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T13:06:18.987506" + "timestamp": "2024-09-17T18:56:30.086204" }, "Params: --min_mapped_reads 90 - stub": { "content": [ + 22, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -1184,14 +1092,12 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.1" + "nf-core/rnaseq": "v3.16.0dev" } }, [ "custom", "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw.html", @@ -1223,13 +1129,14 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ - + "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T13:06:59.786162" + "timestamp": "2024-09-17T18:57:25.990278" } } \ No newline at end of file diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index c0cb4f24e..432541d89 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -13,15 +13,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } @@ -39,15 +40,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index d572e81e3..99bc0303a 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -1,6 +1,7 @@ { "Params: --remove_ribo_rna": { "content": [ + 205, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -139,7 +140,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.1" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -151,8 +152,6 @@ "WT_REP2.stats.txt", "custom", "out", - "genome_gfp.fasta", - "genome_gfp.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw_1_fastqc.html", @@ -192,41 +191,13 @@ "star_salmon", "multiqc_report.html", "multiqc_report_data", - "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "fastqc-status-check-heatmap-1.txt", - "fastqc-status-check-heatmap.txt", - "fastqc_adapter_content_plot.txt", - "fastqc_overrepresented_sequences_plot-1.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot-1.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot-1.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot-1.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot-1.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot-1.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", - "multiqc_citations.txt", - "multiqc_cutadapt.txt", "multiqc_data.json", "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", - "multiqc_fastqc_fastqc_raw.txt", - "multiqc_fastqc_fastqc_trimmed.txt", - "multiqc_featurecounts_biotype_plot.txt", "multiqc_general_stats.txt", "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", @@ -241,7 +212,6 @@ "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", - "multiqc_samtools_idxstats.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sortmerna.txt", @@ -254,16 +224,9 @@ "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", "picard_deduplication.txt", - "picard_histogram.txt", - "picard_histogram_1.txt", - "picard_histogram_2.txt", - "qualimap_gene_coverage_profile_Counts.txt", - "qualimap_gene_coverage_profile_Normalised.txt", "qualimap_genomic_origin.txt", - "qualimap_rnaseq_cov_hist.txt", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", - "rseqc_infer_experiment_plot.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", @@ -279,9 +242,6 @@ "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", "sortmerna-detailed-plot.txt", @@ -356,8 +316,6 @@ "samtools-stats-dp.pdf", "samtools_alignment_plot-cnt.pdf", "samtools_alignment_plot-pct.pdf", - "sortmerna-detailed-plot-cnt.pdf", - "sortmerna-detailed-plot-pct.pdf", "star_alignment_plot-cnt.pdf", "star_alignment_plot-pct.pdf", "star_salmon_deseq2_clustering-plot.pdf", @@ -366,45 +324,21 @@ "png", "cutadapt_filtered_reads_plot-cnt.png", "cutadapt_filtered_reads_plot-pct.png", - "cutadapt_trimmed_sequences_plot_3_Counts.png", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "dupradar-section-plot.png", "fail_strand_check_table.png", - "fastqc-status-check-heatmap-1.png", - "fastqc-status-check-heatmap.png", "fastqc_adapter_content_plot.png", - "fastqc_overrepresented_sequences_plot-1.png", - "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot-1.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot-1.png", "fastqc_per_base_sequence_quality_plot.png", - "fastqc_per_sequence_gc_content_plot-1_Counts.png", - "fastqc_per_sequence_gc_content_plot-1_Percentages.png", - "fastqc_per_sequence_gc_content_plot_Counts.png", - "fastqc_per_sequence_gc_content_plot_Percentages.png", - "fastqc_per_sequence_quality_scores_plot-1.png", - "fastqc_per_sequence_quality_scores_plot.png", - "fastqc_sequence_counts_plot-1-cnt.png", - "fastqc_sequence_counts_plot-1-pct.png", - "fastqc_sequence_counts_plot-cnt.png", - "fastqc_sequence_counts_plot-pct.png", - "fastqc_sequence_duplication_levels_plot-1.png", - "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", - "featurecounts_biotype_plot-cnt.png", - "featurecounts_biotype_plot-pct.png", "general_stats_table.png", "picard_deduplication-cnt.png", "picard_deduplication-pct.png", - "qualimap_gene_coverage_profile_Counts.png", - "qualimap_gene_coverage_profile_Normalised.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", - "rseqc_infer_experiment_plot.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", @@ -416,23 +350,14 @@ "rseqc_junction_saturation_plot_Novel_Junctions.png", "rseqc_read_distribution_plot-cnt.png", "rseqc_read_distribution_plot-pct.png", - "rseqc_read_dups_plot.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png", "samtools-stats-dp.png", "samtools_alignment_plot-cnt.png", "samtools_alignment_plot-pct.png", - "sortmerna-detailed-plot-cnt.png", - "sortmerna-detailed-plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", "star_salmon_deseq2_clustering-plot.png", @@ -506,8 +431,6 @@ "samtools-stats-dp.svg", "samtools_alignment_plot-cnt.svg", "samtools_alignment_plot-pct.svg", - "sortmerna-detailed-plot-cnt.svg", - "sortmerna-detailed-plot-pct.svg", "star_alignment_plot-cnt.svg", "star_alignment_plot-pct.svg", "star_salmon_deseq2_clustering-plot.svg", @@ -518,86 +441,55 @@ "salmon", "RAP1_IAA_30M_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "deseq2_qc", - "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -621,25 +513,14 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", - "tx2gene.tsv", "sortmerna", - "RAP1_IAA_30M_REP1.sortmerna.log", - "RAP1_UNINDUCED_REP1.sortmerna.log", - "RAP1_UNINDUCED_REP2.sortmerna.log", - "WT_REP1.sortmerna.log", - "WT_REP2.sortmerna.log", "star_salmon", "RAP1_IAA_30M_REP1", "RAP1_IAA_30M_REP1.markdup.sorted.bam", "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -650,13 +531,8 @@ "RAP1_UNINDUCED_REP1.markdup.sorted.bam", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -667,13 +543,8 @@ "RAP1_UNINDUCED_REP2.markdup.sorted.bam", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -684,13 +555,8 @@ "WT_REP1.markdup.sorted.bam", "WT_REP1.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -701,13 +567,8 @@ "WT_REP2.markdup.sorted.bam", "WT_REP2.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -726,7 +587,6 @@ "WT_REP2.forward.bigWig", "WT_REP2.reverse.bigWig", "deseq2_qc", - "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -746,11 +606,6 @@ "WT_REP1_duprateExpBoxplot.pdf", "WT_REP2_duprateExpBoxplot.pdf", "gene_data", - "RAP1_IAA_30M_REP1_dupMatrix.txt", - "RAP1_UNINDUCED_REP1_dupMatrix.txt", - "RAP1_UNINDUCED_REP2_dupMatrix.txt", - "WT_REP1_dupMatrix.txt", - "WT_REP2_dupMatrix.txt", "histogram", "RAP1_IAA_30M_REP1_expressionHist.pdf", "RAP1_UNINDUCED_REP1_expressionHist.pdf", @@ -758,11 +613,6 @@ "WT_REP1_expressionHist.pdf", "WT_REP2_expressionHist.pdf", "intercepts_slope", - "RAP1_IAA_30M_REP1_intercept_slope.txt", - "RAP1_UNINDUCED_REP1_intercept_slope.txt", - "RAP1_UNINDUCED_REP2_intercept_slope.txt", - "WT_REP1_intercept_slope.txt", - "WT_REP2_intercept_slope.txt", "scatter_plot", "RAP1_IAA_30M_REP1_duprateExpDens.pdf", "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", @@ -770,47 +620,27 @@ "WT_REP1_duprateExpDens.pdf", "WT_REP2_duprateExpDens.pdf", "featurecounts", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv", - "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv", - "RAP1_IAA_30M_REP1.featureCounts.txt", "RAP1_IAA_30M_REP1.featureCounts.txt.summary", - "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv", - "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv", - "RAP1_UNINDUCED_REP1.featureCounts.txt", "RAP1_UNINDUCED_REP1.featureCounts.txt.summary", - "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv", - "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv", - "RAP1_UNINDUCED_REP2.featureCounts.txt", "RAP1_UNINDUCED_REP2.featureCounts.txt.summary", - "WT_REP1.biotype_counts_mqc.tsv", - "WT_REP1.biotype_counts_rrna_mqc.tsv", - "WT_REP1.featureCounts.txt", "WT_REP1.featureCounts.txt.summary", - "WT_REP2.biotype_counts_mqc.tsv", - "WT_REP2.biotype_counts_rrna_mqc.tsv", - "WT_REP2.featureCounts.txt", "WT_REP2.featureCounts.txt.summary", "log", "RAP1_IAA_30M_REP1.Log.final.out", "RAP1_IAA_30M_REP1.Log.out", "RAP1_IAA_30M_REP1.Log.progress.out", - "RAP1_IAA_30M_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP1.Log.final.out", "RAP1_UNINDUCED_REP1.Log.out", "RAP1_UNINDUCED_REP1.Log.progress.out", - "RAP1_UNINDUCED_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP2.Log.final.out", "RAP1_UNINDUCED_REP2.Log.out", "RAP1_UNINDUCED_REP2.Log.progress.out", - "RAP1_UNINDUCED_REP2.SJ.out.tab", "WT_REP1.Log.final.out", "WT_REP1.Log.out", "WT_REP1.Log.progress.out", - "WT_REP1.SJ.out.tab", "WT_REP2.Log.final.out", "WT_REP2.Log.out", "WT_REP2.Log.progress.out", - "WT_REP2.SJ.out.tab", "picard_metrics", "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -823,190 +653,90 @@ "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "rseqc", "bam_stat", @@ -1016,11 +746,6 @@ "WT_REP1.bam_stat.txt", "WT_REP2.bam_stat.txt", "infer_experiment", - "RAP1_IAA_30M_REP1.infer_experiment.txt", - "RAP1_UNINDUCED_REP1.infer_experiment.txt", - "RAP1_UNINDUCED_REP2.infer_experiment.txt", - "WT_REP1.infer_experiment.txt", - "WT_REP2.infer_experiment.txt", "inner_distance", "pdf", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", @@ -1169,51 +894,30 @@ "WT_REP2.sorted.bam.stats", "stringtie", "RAP1_IAA_30M_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_IAA_30M_REP1.coverage.gtf", "RAP1_IAA_30M_REP1.gene.abundance.txt", "RAP1_IAA_30M_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP1.coverage.gtf", "RAP1_UNINDUCED_REP1.gene.abundance.txt", "RAP1_UNINDUCED_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP2.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP2.coverage.gtf", "RAP1_UNINDUCED_REP2.gene.abundance.txt", "RAP1_UNINDUCED_REP2.transcripts.gtf", "WT_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "WT_REP1.coverage.gtf", "WT_REP1.gene.abundance.txt", "WT_REP1.transcripts.gtf", "WT_REP2.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "WT_REP2.coverage.gtf", "WT_REP2.gene.abundance.txt", "WT_REP2.transcripts.gtf", - "tx2gene.tsv", "trimgalore", "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", @@ -1225,6 +929,8 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ + "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", + "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -1264,32 +970,106 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,53addd7b78d8ae224920ec9b97489d72", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,97fc7bde65a7efc5ab3af48ef0400c20", + "sortmerna-detailed-plot-cnt.pdf:md5,45068e9eb0457fa236aa842eb20e6579", + "sortmerna-detailed-plot-pct.pdf:md5,141dbadd12bdfe5e424089f547ae9241", + "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", + "dupradar-section-plot.png:md5,62ee84d3b32bdbfb9766fa970680f92c", + "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890", + "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84", + "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f", + "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14", + "fastqc_per_sequence_gc_content_plot-1_Counts.png:md5,8a806cec2142f9911502e0a253d83d13", + "fastqc_per_sequence_gc_content_plot-1_Percentages.png:md5,953929d50c8490029880e205e4db7959", + "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16", + "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,eba3abf8bedb2cb20bad90c54e9c8881", + "fastqc_per_sequence_quality_scores_plot-1.png:md5,d2c29cae169f35744500c751b4a7366e", + "fastqc_per_sequence_quality_scores_plot.png:md5,42fd7369a8aca78f620164a9e887c3cb", + "fastqc_sequence_counts_plot-1-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", + "fastqc_sequence_counts_plot-1-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", + "fastqc_sequence_counts_plot-cnt.png:md5,3890d5555f2a39b46b9f6efb14cb91f2", + "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054", + "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", + "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", + "featurecounts_biotype_plot-cnt.png:md5,ed2c5826034fcf2417afe79902897c45", + "featurecounts_biotype_plot-pct.png:md5,96abf028d347f568289b3a741aa8c08d", + "qualimap_gene_coverage_profile_Counts.png:md5,fb739f4297a156f0913f21f20090f598", + "qualimap_gene_coverage_profile_Normalised.png:md5,710960caa692f0d0eceadcc83650cf00", + "rseqc_infer_experiment_plot.png:md5,49f1faa0849545b8a75af2657d0ee5fa", + "rseqc_read_dups_plot.png:md5,1a18ce4ca5f36722f1fdd579d7eb41e1", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,af332971e3158b3cfee3a65311ebfe2c", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,f12bcf930eac8ed45da7b4668b1169c8", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,ff8e0f61b02f8c9abcce5e83214c87fd", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,1a029e5d23f82d537470363a065b644a", + "sortmerna-detailed-plot-cnt.png:md5,3875997f21c98e8906cd182d959e0020", + "sortmerna-detailed-plot-pct.png:md5,971398875e5cbd50313b6fee7eeb302c", + "sortmerna-detailed-plot-cnt.svg:md5,4cf8f33f9c4b5fa32ca5fa0f1da34521", + "sortmerna-detailed-plot-pct.svg:md5,9e3e7732d400e8fed44bd9b5442f7f9e", "ambig_info.tsv:md5,25ced9693254994a7878241225baabb6", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + 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"down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", + "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", + "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", + "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", + "Coverage Profile Along Genes (High).png:md5,3c1c603d63f3f7f9ba1ab6e7749b7771", + "Coverage Profile Along Genes (Low).png:md5,9f80251ed043cf900fa939cc254ccc81", + "Coverage Profile Along Genes (Total).png:md5,a420f287f986a8db317be712ac0a2237", + "Transcript coverage histogram.png:md5,c467c5eac12a95f8569198927434440d", "coverage_profile_along_genes_(high).txt:md5,3f76529bd723d5320c86cc407fbb3294", "coverage_profile_along_genes_(low).txt:md5,b9be191fdec82c78057e083d3adf20dd", "coverage_profile_along_genes_(total).txt:md5,b9be191fdec82c78057e083d3adf20dd", @@ -1335,6 +1205,26 @@ "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,484e2860c6c496b1da5fac475a0cd3e4", "WT_REP1.infer_experiment.txt:md5,298c430c61cb7a46b48af867a0dfe00b", "WT_REP2.infer_experiment.txt:md5,18758f433cf5c19bce599e5329da39a9", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,ee43fdd5d543e24c53b6031cdbabb656", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,a052ab04070e72cc318fb7680b0764e3", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,52a62313943891cc8dcb3b4c1e117f18", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,d279003d92f7feef9adb31203f84474a", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,3c7b9cf3bb1dcb98d79f8226eef7aa4c", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,682817a9d0a1ac9c1637249e007d3514", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,907ab2e06346df131cbdb929afc005a8", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,f2cf8aa2786c710fb6be5857e1545e0e", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,041edee3193df311f621c09f4991892b", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], @@ -1342,10 +1232,11 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T13:18:05.873394" + "timestamp": "2024-09-17T19:09:08.723809" }, "Params: --remove_ribo_rna - stub": { "content": [ + 24, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -1390,14 +1281,12 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.1" + "nf-core/rnaseq": "v3.16.0dev" } }, [ "custom", "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw.html", @@ -1429,13 +1318,14 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ - + "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T13:18:51.223833" + "timestamp": "2024-09-17T19:10:02.333783" } } \ No newline at end of file diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index 530ce5ed3..f543cd932 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -15,15 +15,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } @@ -43,15 +44,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 73abab293..a79bb4ec9 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -1,6 +1,7 @@ { "Params: --pseudo_aligner salmon --skip_qc --skip_alignment": { "content": [ + 34, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -49,7 +50,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.1" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -61,8 +62,6 @@ "WT_REP2.stats.txt", "custom", "out", - "genome_gfp.fasta", - "genome_gfp.gtf", "fastqc", "trim", "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", @@ -84,24 +83,8 @@ "multiqc", "multiqc_report.html", "multiqc_report_data", - "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "fastqc-status-check-heatmap.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table.txt", - "multiqc_citations.txt", - "multiqc_cutadapt.txt", "multiqc_data.json", - "multiqc_fastqc_fastqc_trimmed.txt", "multiqc_general_stats.txt", "multiqc_salmon.txt", "multiqc_software_versions.txt", @@ -130,18 +113,8 @@ "png", "cutadapt_filtered_reads_plot-cnt.png", "cutadapt_filtered_reads_plot-pct.png", - "cutadapt_trimmed_sequences_plot_3_Counts.png", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "fastqc-status-check-heatmap.png", - "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot.png", - "fastqc_per_sequence_gc_content_plot_Counts.png", - "fastqc_per_sequence_gc_content_plot_Percentages.png", - "fastqc_per_sequence_quality_scores_plot.png", - "fastqc_sequence_counts_plot-cnt.png", - "fastqc_sequence_counts_plot-pct.png", - "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", @@ -170,80 +143,50 @@ "salmon", "RAP1_IAA_30M_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", @@ -260,7 +203,6 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", - "tx2gene.tsv", "trimgalore", "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", @@ -272,6 +214,8 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ + "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", + "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -288,19 +232,44 @@ "multiqc_citations.txt:md5,f789abe663d4b4214f0ddeb413a7f150", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", + "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", + "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890", + "fastqc_overrepresented_sequences_plot.png:md5,40e450251b80ec0efc9364434234ec7f", + "fastqc_per_sequence_gc_content_plot_Counts.png:md5,8a806cec2142f9911502e0a253d83d13", + "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,953929d50c8490029880e205e4db7959", + "fastqc_per_sequence_quality_scores_plot.png:md5,d2c29cae169f35744500c751b4a7366e", + "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", + "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", + "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" @@ -310,10 +279,11 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T13:21:46.987509" + "timestamp": "2024-09-17T19:13:06.946699" }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ + 16, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -347,14 +317,12 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.1" + "nf-core/rnaseq": "v3.16.0dev" } }, [ "custom", "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", "fastqc", "trim", "multiqc", @@ -374,13 +342,14 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ - + "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T13:22:21.275937" + "timestamp": "2024-09-17T19:14:07.935482" } } \ No newline at end of file diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index fc372d235..1ea1c66ad 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -13,15 +13,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } @@ -39,15 +40,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index bb5be7bfd..cfd6fbaea 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -1,6 +1,7 @@ { "Params: --skip_qc - stub": { "content": [ + 17, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -39,14 +40,12 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.1" + "nf-core/rnaseq": "v3.16.0dev" } }, [ "custom", "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", "fastqc", "trim", "multiqc", @@ -67,17 +66,19 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ - + "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T13:28:26.396195" + "timestamp": "2024-09-17T19:24:13.457444" }, "Params: --skip_qc": { "content": [ + 136, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -166,7 +167,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.1" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -178,8 +179,6 @@ "WT_REP2.stats.txt", "custom", "out", - "genome_gfp.fasta", - "genome_gfp.gtf", "fastqc", "trim", "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", @@ -202,43 +201,20 @@ "star_salmon", "multiqc_report.html", "multiqc_report_data", - "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "fastqc-status-check-heatmap.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table.txt", - "multiqc_citations.txt", - "multiqc_cutadapt.txt", "multiqc_data.json", - "multiqc_fastqc_fastqc_trimmed.txt", "multiqc_general_stats.txt", "multiqc_picard_dups.txt", "multiqc_salmon.txt", "multiqc_samtools_flagstat.txt", - "multiqc_samtools_idxstats.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", "multiqc_star.txt", "picard_deduplication.txt", - "picard_histogram.txt", - "picard_histogram_1.txt", - "picard_histogram_2.txt", "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", "star_alignment_plot.txt", @@ -282,18 +258,8 @@ "png", "cutadapt_filtered_reads_plot-cnt.png", "cutadapt_filtered_reads_plot-pct.png", - "cutadapt_trimmed_sequences_plot_3_Counts.png", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "fastqc-status-check-heatmap.png", - "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot.png", - "fastqc_per_sequence_gc_content_plot_Counts.png", - "fastqc_per_sequence_gc_content_plot_Percentages.png", - "fastqc_per_sequence_quality_scores_plot.png", - "fastqc_sequence_counts_plot-cnt.png", - "fastqc_sequence_counts_plot-pct.png", - "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", @@ -302,12 +268,6 @@ "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png", "samtools-stats-dp.png", "samtools_alignment_plot-cnt.png", "samtools_alignment_plot-pct.png", @@ -354,80 +314,50 @@ "salmon", "RAP1_IAA_30M_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", @@ -444,19 +374,13 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", - "tx2gene.tsv", "star_salmon", "RAP1_IAA_30M_REP1", "RAP1_IAA_30M_REP1.markdup.sorted.bam", "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -467,13 +391,8 @@ "RAP1_UNINDUCED_REP1.markdup.sorted.bam", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -484,13 +403,8 @@ "RAP1_UNINDUCED_REP2.markdup.sorted.bam", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -501,13 +415,8 @@ "WT_REP1.markdup.sorted.bam", "WT_REP1.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -518,13 +427,8 @@ "WT_REP2.markdup.sorted.bam", "WT_REP2.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -546,23 +450,18 @@ "RAP1_IAA_30M_REP1.Log.final.out", "RAP1_IAA_30M_REP1.Log.out", "RAP1_IAA_30M_REP1.Log.progress.out", - "RAP1_IAA_30M_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP1.Log.final.out", "RAP1_UNINDUCED_REP1.Log.out", "RAP1_UNINDUCED_REP1.Log.progress.out", - "RAP1_UNINDUCED_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP2.Log.final.out", "RAP1_UNINDUCED_REP2.Log.out", "RAP1_UNINDUCED_REP2.Log.progress.out", - "RAP1_UNINDUCED_REP2.SJ.out.tab", "WT_REP1.Log.final.out", "WT_REP1.Log.out", "WT_REP1.Log.progress.out", - "WT_REP1.SJ.out.tab", "WT_REP2.Log.final.out", "WT_REP2.Log.out", "WT_REP2.Log.progress.out", - "WT_REP2.SJ.out.tab", "picard_metrics", "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -614,51 +513,30 @@ "WT_REP2.sorted.bam.stats", "stringtie", "RAP1_IAA_30M_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_IAA_30M_REP1.coverage.gtf", "RAP1_IAA_30M_REP1.gene.abundance.txt", "RAP1_IAA_30M_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP1.coverage.gtf", "RAP1_UNINDUCED_REP1.gene.abundance.txt", "RAP1_UNINDUCED_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP2.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP2.coverage.gtf", "RAP1_UNINDUCED_REP2.gene.abundance.txt", "RAP1_UNINDUCED_REP2.transcripts.gtf", "WT_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "WT_REP1.coverage.gtf", "WT_REP1.gene.abundance.txt", "WT_REP1.transcripts.gtf", "WT_REP2.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "WT_REP2.coverage.gtf", "WT_REP2.gene.abundance.txt", "WT_REP2.transcripts.gtf", - "tx2gene.tsv", "trimgalore", "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", @@ -670,6 +548,8 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ + "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", + "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -693,32 +573,103 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", + "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890", + "fastqc_overrepresented_sequences_plot.png:md5,40e450251b80ec0efc9364434234ec7f", + "fastqc_per_sequence_gc_content_plot_Counts.png:md5,8a806cec2142f9911502e0a253d83d13", + "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,953929d50c8490029880e205e4db7959", + "fastqc_per_sequence_quality_scores_plot.png:md5,d2c29cae169f35744500c751b4a7366e", + "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", + "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", + "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,d5d8a85b7ad72a0cb93d9283ea12b23f", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,a6849cd92ae738441212b681a411614d", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", + "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", + "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", + "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204", + "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,3f149502efe2a9d4bac98b1dd18c15e7", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,a052ab04070e72cc318fb7680b0764e3", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,e82329a443b9ff50a86e42aff91bd704", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,d279003d92f7feef9adb31203f84474a", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,10e2d00f93f9e74f224bd3c1bfbeb29b", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,9aa371befc36478d7720d3ea275e6f4d", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,907ab2e06346df131cbdb929afc005a8", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,b03f3118d1aa58fceadcb3311028e856", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,041edee3193df311f621c09f4991892b", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], @@ -726,6 +677,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T13:27:46.913014" + "timestamp": "2024-09-17T19:23:30.52516" } } \ No newline at end of file diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index a00a104ed..abd2376f6 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -13,15 +13,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 098bbe78a..8c091316e 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -1,6 +1,7 @@ { "Params: --skip_trimming": { "content": [ + 193, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -129,7 +130,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.1" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -141,8 +142,6 @@ "WT_REP2.stats.txt", "custom", "out", - "genome_gfp.fasta", - "genome_gfp.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw_1_fastqc.html", @@ -165,25 +164,12 @@ "star_salmon", "multiqc_report.html", "multiqc_report_data", - "fastqc-status-check-heatmap.txt", - "fastqc_adapter_content_plot.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", - "multiqc_citations.txt", "multiqc_data.json", "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", - "multiqc_fastqc_fastqc_raw.txt", - "multiqc_featurecounts_biotype_plot.txt", "multiqc_general_stats.txt", "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", @@ -198,7 +184,6 @@ "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", - "multiqc_samtools_idxstats.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", @@ -210,16 +195,9 @@ "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", "picard_deduplication.txt", - "picard_histogram.txt", - "picard_histogram_1.txt", - "picard_histogram_2.txt", - "qualimap_gene_coverage_profile_Counts.txt", - "qualimap_gene_coverage_profile_Normalised.txt", "qualimap_genomic_origin.txt", - "qualimap_rnaseq_cov_hist.txt", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", - "rseqc_infer_experiment_plot.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", @@ -235,9 +213,6 @@ "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", "star_alignment_plot.txt", @@ -301,31 +276,17 @@ "star_salmon_deseq2_pca-plot.pdf", "star_summary_table.pdf", "png", - "dupradar-section-plot.png", "fail_strand_check_table.png", - "fastqc-status-check-heatmap.png", "fastqc_adapter_content_plot.png", - "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot.png", - "fastqc_per_sequence_gc_content_plot_Counts.png", - "fastqc_per_sequence_gc_content_plot_Percentages.png", - "fastqc_per_sequence_quality_scores_plot.png", - "fastqc_sequence_counts_plot-cnt.png", - "fastqc_sequence_counts_plot-pct.png", - "fastqc_sequence_duplication_levels_plot.png", "fastqc_top_overrepresented_sequences_table.png", - "featurecounts_biotype_plot-cnt.png", - "featurecounts_biotype_plot-pct.png", "general_stats_table.png", "picard_deduplication-cnt.png", "picard_deduplication-pct.png", - "qualimap_gene_coverage_profile_Counts.png", - "qualimap_gene_coverage_profile_Normalised.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", - "rseqc_infer_experiment_plot.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", @@ -337,18 +298,11 @@ "rseqc_junction_saturation_plot_Novel_Junctions.png", "rseqc_read_distribution_plot-cnt.png", "rseqc_read_distribution_plot-pct.png", - "rseqc_read_dups_plot.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png", "samtools-stats-dp.png", "samtools_alignment_plot-cnt.png", "samtools_alignment_plot-pct.png", @@ -419,86 +373,55 @@ "salmon", "RAP1_IAA_30M_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "deseq2_qc", - "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -522,19 +445,13 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", - "tx2gene.tsv", "star_salmon", "RAP1_IAA_30M_REP1", "RAP1_IAA_30M_REP1.markdup.sorted.bam", "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -545,13 +462,8 @@ "RAP1_UNINDUCED_REP1.markdup.sorted.bam", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -562,13 +474,8 @@ "RAP1_UNINDUCED_REP2.markdup.sorted.bam", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -579,13 +486,8 @@ "WT_REP1.markdup.sorted.bam", "WT_REP1.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -596,13 +498,8 @@ "WT_REP2.markdup.sorted.bam", "WT_REP2.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -621,7 +518,6 @@ "WT_REP2.forward.bigWig", "WT_REP2.reverse.bigWig", "deseq2_qc", - "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -641,11 +537,6 @@ "WT_REP1_duprateExpBoxplot.pdf", "WT_REP2_duprateExpBoxplot.pdf", "gene_data", - "RAP1_IAA_30M_REP1_dupMatrix.txt", - "RAP1_UNINDUCED_REP1_dupMatrix.txt", - "RAP1_UNINDUCED_REP2_dupMatrix.txt", - "WT_REP1_dupMatrix.txt", - "WT_REP2_dupMatrix.txt", "histogram", "RAP1_IAA_30M_REP1_expressionHist.pdf", "RAP1_UNINDUCED_REP1_expressionHist.pdf", @@ -653,11 +544,6 @@ "WT_REP1_expressionHist.pdf", "WT_REP2_expressionHist.pdf", "intercepts_slope", - "RAP1_IAA_30M_REP1_intercept_slope.txt", - "RAP1_UNINDUCED_REP1_intercept_slope.txt", - "RAP1_UNINDUCED_REP2_intercept_slope.txt", - "WT_REP1_intercept_slope.txt", - "WT_REP2_intercept_slope.txt", "scatter_plot", "RAP1_IAA_30M_REP1_duprateExpDens.pdf", "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", @@ -665,47 +551,27 @@ "WT_REP1_duprateExpDens.pdf", "WT_REP2_duprateExpDens.pdf", "featurecounts", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv", - "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv", - "RAP1_IAA_30M_REP1.featureCounts.txt", "RAP1_IAA_30M_REP1.featureCounts.txt.summary", - "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv", - "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv", - "RAP1_UNINDUCED_REP1.featureCounts.txt", "RAP1_UNINDUCED_REP1.featureCounts.txt.summary", - "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv", - "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv", - "RAP1_UNINDUCED_REP2.featureCounts.txt", "RAP1_UNINDUCED_REP2.featureCounts.txt.summary", - "WT_REP1.biotype_counts_mqc.tsv", - "WT_REP1.biotype_counts_rrna_mqc.tsv", - "WT_REP1.featureCounts.txt", "WT_REP1.featureCounts.txt.summary", - "WT_REP2.biotype_counts_mqc.tsv", - "WT_REP2.biotype_counts_rrna_mqc.tsv", - "WT_REP2.featureCounts.txt", "WT_REP2.featureCounts.txt.summary", "log", "RAP1_IAA_30M_REP1.Log.final.out", "RAP1_IAA_30M_REP1.Log.out", "RAP1_IAA_30M_REP1.Log.progress.out", - "RAP1_IAA_30M_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP1.Log.final.out", "RAP1_UNINDUCED_REP1.Log.out", "RAP1_UNINDUCED_REP1.Log.progress.out", - "RAP1_UNINDUCED_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP2.Log.final.out", "RAP1_UNINDUCED_REP2.Log.out", "RAP1_UNINDUCED_REP2.Log.progress.out", - "RAP1_UNINDUCED_REP2.SJ.out.tab", "WT_REP1.Log.final.out", "WT_REP1.Log.out", "WT_REP1.Log.progress.out", - "WT_REP1.SJ.out.tab", "WT_REP2.Log.final.out", "WT_REP2.Log.out", "WT_REP2.Log.progress.out", - "WT_REP2.SJ.out.tab", "picard_metrics", "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -718,190 +584,90 @@ "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "rseqc", "bam_stat", @@ -911,11 +677,6 @@ "WT_REP1.bam_stat.txt", "WT_REP2.bam_stat.txt", "infer_experiment", - "RAP1_IAA_30M_REP1.infer_experiment.txt", - "RAP1_UNINDUCED_REP1.infer_experiment.txt", - "RAP1_UNINDUCED_REP2.infer_experiment.txt", - "WT_REP1.infer_experiment.txt", - "WT_REP2.infer_experiment.txt", "inner_distance", "pdf", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", @@ -1064,53 +825,34 @@ "WT_REP2.sorted.bam.stats", "stringtie", "RAP1_IAA_30M_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_IAA_30M_REP1.coverage.gtf", "RAP1_IAA_30M_REP1.gene.abundance.txt", "RAP1_IAA_30M_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP1.coverage.gtf", "RAP1_UNINDUCED_REP1.gene.abundance.txt", "RAP1_UNINDUCED_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP2.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP2.coverage.gtf", "RAP1_UNINDUCED_REP2.gene.abundance.txt", "RAP1_UNINDUCED_REP2.transcripts.gtf", "WT_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "WT_REP1.coverage.gtf", "WT_REP1.gene.abundance.txt", "WT_REP1.transcripts.gtf", "WT_REP2.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "WT_REP2.coverage.gtf", "WT_REP2.gene.abundance.txt", - "WT_REP2.transcripts.gtf", - "tx2gene.tsv" + "WT_REP2.transcripts.gtf" ], [ + "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", + "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", @@ -1135,32 +877,85 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,a557130553131c893398532377d3b525", + "dupradar-section-plot.png:md5,5e5487f0e1f1521264462d5cb9ee9089", + "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84", + "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14", + "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16", + "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,eba3abf8bedb2cb20bad90c54e9c8881", + "fastqc_per_sequence_quality_scores_plot.png:md5,42fd7369a8aca78f620164a9e887c3cb", + "fastqc_sequence_counts_plot-cnt.png:md5,3890d5555f2a39b46b9f6efb14cb91f2", + "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054", + "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", + "featurecounts_biotype_plot-cnt.png:md5,dcb37b4ce2fff5ca2e22767b172e55a8", + "featurecounts_biotype_plot-pct.png:md5,b15370ba2c056815939251f820d9e2af", + "qualimap_gene_coverage_profile_Counts.png:md5,8312f777db61509caa66d1f53a4b6b07", + "qualimap_gene_coverage_profile_Normalised.png:md5,66acb12427130766801a8376f95ed88b", + "rseqc_infer_experiment_plot.png:md5,c3108e35020ee93a77a62ea0167613b2", + "rseqc_read_dups_plot.png:md5,1e43ad78c4a87f7736b552ad71d25c16", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,d5d8a85b7ad72a0cb93d9283ea12b23f", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,64f2501f91db6dd0edd5e49c0b9ca8b7", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,52f30fc3448f43735ce9eca54b306c8e", "ambig_info.tsv:md5,e099a9ec06de792219139248712f7f40", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", "lib_format_counts.json:md5,406e1457f0f0506bd8e605a217477436", "ambig_info.tsv:md5,0e0895adb376929bec8e0dd0677bf7d8", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", "lib_format_counts.json:md5,afd2a0ddf0fd0ec4f99be898608a59db", "ambig_info.tsv:md5,6ed1b46c69917d6af3f093f9503bb962", + 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"R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "ambig_info.tsv:md5,d1d3bd2a5617220b29a9063cb29f0578", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", "ambig_info.tsv:md5,452bbc83465339d2467663b061400b95", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", "ambig_info.tsv:md5,f2aed38ba5251664024392bc89ae3f01", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", 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"coverage_profile_along_genes_(low).txt:md5,031046ef33de379e0463fddc0b924ecd", "coverage_profile_along_genes_(total).txt:md5,031046ef33de379e0463fddc0b924ecd", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", + "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + "comment.png:md5,882e40f3d6a16c6ed35659b105251525", + "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", + "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", + "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", + "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", + "Coverage Profile Along Genes (High).png:md5,75dbf9d2b8bde265fdda486c050d5ff5", + "Coverage Profile Along Genes 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"comment.png:md5,882e40f3d6a16c6ed35659b105251525", + "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", + "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", + "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", + "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", + "Coverage Profile Along Genes (High).png:md5,f9f0caee3156d32588c12daab8895a0f", + "Coverage Profile Along Genes (Low).png:md5,35ac4785ed0ffb80aaeec1fb26825f4b", + "Coverage Profile Along Genes (Total).png:md5,781cc1b68e9f7afc30a84b7e45b06f85", + "Transcript coverage histogram.png:md5,a4a300dc782deea67f18e516e0c50b3b", "coverage_profile_along_genes_(high).txt:md5,f7c11dace9fc4f446fc29e5db7b3ee24", "coverage_profile_along_genes_(low).txt:md5,f53cfe3e30c560e3261818c2e6df3d5d", "coverage_profile_along_genes_(total).txt:md5,f53cfe3e30c560e3261818c2e6df3d5d", @@ -1206,6 +1091,26 @@ "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,be4b322faffa736ab6ac39ff39c7aa9d", "WT_REP1.infer_experiment.txt:md5,7e8c79fa27780693523ad7acd8f109c4", "WT_REP2.infer_experiment.txt:md5,c895dbd41b5a075ad4032e2732145b6a", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,9225250f729f9688c50718ad82989f4c", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,319f3eaf67c02b6198a4d746f8b11a44", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,1c69593079c7bff8b3e36b9d9aa616f9", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,db2e9c245b5db90551b83c799194113c", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,9628d551f88776248ace242ba43978e3", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,50d273bef261ddb395260dc74eff1a8b", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,9c0bf54804f5624b567481de8f5a5ae4", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,d92fcfde4016a15c3f54340e8637e554", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,3bddb4b7381a62a0104b7004e5b71f20", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,cd4c62717bb0a0db1a17e9c6d8788599", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], @@ -1213,7 +1118,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T13:34:58.344727" - + "timestamp": "2024-09-17T19:30:48.005426" } } \ No newline at end of file diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index b6421cb93..8f5a82e6b 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -13,15 +13,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } @@ -39,15 +40,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 756aa96fb..14112208c 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -1,6 +1,7 @@ { "Params: --aligner star_rsem": { "content": [ + 188, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -133,7 +134,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.1" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -145,8 +146,6 @@ "WT_REP2.stats.txt", "custom", "out", - "genome_gfp.fasta", - "genome_gfp.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw_1_fastqc.html", @@ -186,41 +185,13 @@ "star_rsem", "multiqc_report.html", "multiqc_report_data", - "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "fastqc-status-check-heatmap-1.txt", - "fastqc-status-check-heatmap.txt", - "fastqc_adapter_content_plot.txt", - "fastqc_overrepresented_sequences_plot-1.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot-1.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot-1.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot-1.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot-1.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot-1.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", - "multiqc_citations.txt", - "multiqc_cutadapt.txt", "multiqc_data.json", "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", - "multiqc_fastqc_fastqc_raw.txt", - "multiqc_fastqc_fastqc_trimmed.txt", - "multiqc_featurecounts_biotype_plot.txt", "multiqc_general_stats.txt", "multiqc_picard_dups.txt", "multiqc_rsem.txt", @@ -236,29 +207,15 @@ "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", - "multiqc_samtools_idxstats.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", - "multiqc_star_rsem_deseq2_clustering-plot.txt", - "multiqc_star_rsem_deseq2_clustering-plot_1.txt", - "multiqc_star_rsem_deseq2_clustering-plot_2.txt", - "multiqc_star_rsem_deseq2_clustering-plot_3.txt", - "multiqc_star_rsem_deseq2_clustering-plot_4.txt", - "multiqc_star_rsem_deseq2_pca-plot.txt", "picard_deduplication.txt", - "picard_histogram.txt", - "picard_histogram_1.txt", - "picard_histogram_2.txt", - "qualimap_gene_coverage_profile_Counts.txt", - "qualimap_gene_coverage_profile_Normalised.txt", "qualimap_genomic_origin.txt", - "qualimap_rnaseq_cov_hist.txt", "qualimap_rnaseq_genome_results.txt", "rsem_assignment_plot.txt", "rsem_multimapping_rates.txt", "rseqc_bam_stat.txt", - "rseqc_infer_experiment_plot.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", @@ -274,9 +231,6 @@ "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", "multiqc_report_plots", @@ -320,9 +274,6 @@ "qualimap_gene_coverage_profile_Normalised.pdf", "qualimap_genomic_origin-cnt.pdf", "qualimap_genomic_origin-pct.pdf", - "rsem_assignment_plot-cnt.pdf", - "rsem_assignment_plot-pct.pdf", - "rsem_multimapping_rates.pdf", "rseqc_bam_stat.pdf", "rseqc_infer_experiment_plot.pdf", "rseqc_inner_distance_plot_Counts.pdf", @@ -351,53 +302,24 @@ "samtools-stats-dp.pdf", "samtools_alignment_plot-cnt.pdf", "samtools_alignment_plot-pct.pdf", - "star_rsem_deseq2_clustering-plot.pdf", - "star_rsem_deseq2_pca-plot.pdf", "png", "cutadapt_filtered_reads_plot-cnt.png", "cutadapt_filtered_reads_plot-pct.png", - "cutadapt_trimmed_sequences_plot_3_Counts.png", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "dupradar-section-plot.png", "fail_strand_check_table.png", - "fastqc-status-check-heatmap-1.png", - "fastqc-status-check-heatmap.png", "fastqc_adapter_content_plot.png", - "fastqc_overrepresented_sequences_plot-1.png", - "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot-1.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot-1.png", "fastqc_per_base_sequence_quality_plot.png", - "fastqc_per_sequence_gc_content_plot-1_Counts.png", - "fastqc_per_sequence_gc_content_plot-1_Percentages.png", - "fastqc_per_sequence_gc_content_plot_Counts.png", - "fastqc_per_sequence_gc_content_plot_Percentages.png", - "fastqc_per_sequence_quality_scores_plot-1.png", - "fastqc_per_sequence_quality_scores_plot.png", - "fastqc_sequence_counts_plot-1-cnt.png", - "fastqc_sequence_counts_plot-1-pct.png", - "fastqc_sequence_counts_plot-cnt.png", - "fastqc_sequence_counts_plot-pct.png", - "fastqc_sequence_duplication_levels_plot-1.png", - "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", - "featurecounts_biotype_plot-cnt.png", - "featurecounts_biotype_plot-pct.png", "general_stats_table.png", "picard_deduplication-cnt.png", "picard_deduplication-pct.png", - "qualimap_gene_coverage_profile_Counts.png", - "qualimap_gene_coverage_profile_Normalised.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", - "rsem_assignment_plot-cnt.png", - "rsem_assignment_plot-pct.png", - "rsem_multimapping_rates.png", "rseqc_bam_stat.png", - "rseqc_infer_experiment_plot.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", @@ -409,23 +331,14 @@ "rseqc_junction_saturation_plot_Novel_Junctions.png", "rseqc_read_distribution_plot-cnt.png", "rseqc_read_distribution_plot-pct.png", - "rseqc_read_dups_plot.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png", "samtools-stats-dp.png", "samtools_alignment_plot-cnt.png", "samtools_alignment_plot-pct.png", - "star_rsem_deseq2_clustering-plot.png", - "star_rsem_deseq2_pca-plot.png", "svg", "cutadapt_filtered_reads_plot-cnt.svg", "cutadapt_filtered_reads_plot-pct.svg", @@ -466,9 +379,6 @@ "qualimap_gene_coverage_profile_Normalised.svg", "qualimap_genomic_origin-cnt.svg", "qualimap_genomic_origin-pct.svg", - "rsem_assignment_plot-cnt.svg", - "rsem_assignment_plot-pct.svg", - "rsem_multimapping_rates.svg", "rseqc_bam_stat.svg", "rseqc_infer_experiment_plot.svg", "rseqc_inner_distance_plot_Counts.svg", @@ -497,93 +407,60 @@ "samtools-stats-dp.svg", "samtools_alignment_plot-cnt.svg", "samtools_alignment_plot-pct.svg", - "star_rsem_deseq2_clustering-plot.svg", - "star_rsem_deseq2_pca-plot.svg", "pipeline_info", "nf_core_rnaseq_software_mqc_versions.yml", "salmon", "RAP1_IAA_30M_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "deseq2_qc", - "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -607,7 +484,6 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", - "tx2gene.tsv", "star_rsem", "RAP1_IAA_30M_REP1.genes.results", "RAP1_IAA_30M_REP1.isoforms.results", @@ -661,7 +537,6 @@ "WT_REP2.forward.bigWig", "WT_REP2.reverse.bigWig", "deseq2_qc", - "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -681,11 +556,6 @@ "WT_REP1_duprateExpBoxplot.pdf", "WT_REP2_duprateExpBoxplot.pdf", "gene_data", - "RAP1_IAA_30M_REP1_dupMatrix.txt", - "RAP1_UNINDUCED_REP1_dupMatrix.txt", - "RAP1_UNINDUCED_REP2_dupMatrix.txt", - "WT_REP1_dupMatrix.txt", - "WT_REP2_dupMatrix.txt", "histogram", "RAP1_IAA_30M_REP1_expressionHist.pdf", "RAP1_UNINDUCED_REP1_expressionHist.pdf", @@ -693,11 +563,6 @@ "WT_REP1_expressionHist.pdf", "WT_REP2_expressionHist.pdf", "intercepts_slope", - "RAP1_IAA_30M_REP1_intercept_slope.txt", - "RAP1_UNINDUCED_REP1_intercept_slope.txt", - "RAP1_UNINDUCED_REP2_intercept_slope.txt", - "WT_REP1_intercept_slope.txt", - "WT_REP2_intercept_slope.txt", "scatter_plot", "RAP1_IAA_30M_REP1_duprateExpDens.pdf", "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", @@ -705,32 +570,12 @@ "WT_REP1_duprateExpDens.pdf", "WT_REP2_duprateExpDens.pdf", "featurecounts", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv", - "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv", - "RAP1_IAA_30M_REP1.featureCounts.txt", "RAP1_IAA_30M_REP1.featureCounts.txt.summary", - "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv", - "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv", - "RAP1_UNINDUCED_REP1.featureCounts.txt", "RAP1_UNINDUCED_REP1.featureCounts.txt.summary", - "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv", - "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv", - "RAP1_UNINDUCED_REP2.featureCounts.txt", "RAP1_UNINDUCED_REP2.featureCounts.txt.summary", - "WT_REP1.biotype_counts_mqc.tsv", - "WT_REP1.biotype_counts_rrna_mqc.tsv", - "WT_REP1.featureCounts.txt", "WT_REP1.featureCounts.txt.summary", - "WT_REP2.biotype_counts_mqc.tsv", - "WT_REP2.biotype_counts_rrna_mqc.tsv", - "WT_REP2.featureCounts.txt", "WT_REP2.featureCounts.txt.summary", "log", - "RAP1_IAA_30M_REP1.log", - "RAP1_UNINDUCED_REP1.log", - "RAP1_UNINDUCED_REP2.log", - "WT_REP1.log", - "WT_REP2.log", "picard_metrics", "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -743,195 +588,91 @@ "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", - "rsem.merged.gene_counts.tsv", - "rsem.merged.gene_tpm.tsv", - "rsem.merged.transcript_counts.tsv", - "rsem.merged.transcript_tpm.tsv", "rseqc", "bam_stat", "RAP1_IAA_30M_REP1.bam_stat.txt", @@ -940,11 +681,6 @@ "WT_REP1.bam_stat.txt", "WT_REP2.bam_stat.txt", "infer_experiment", - "RAP1_IAA_30M_REP1.infer_experiment.txt", - "RAP1_UNINDUCED_REP1.infer_experiment.txt", - "RAP1_UNINDUCED_REP2.infer_experiment.txt", - "WT_REP1.infer_experiment.txt", - "WT_REP2.infer_experiment.txt", "inner_distance", "pdf", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", @@ -1081,46 +817,26 @@ "WT_REP2.sorted.bam.stats", "stringtie", "RAP1_IAA_30M_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_IAA_30M_REP1.coverage.gtf", "RAP1_IAA_30M_REP1.gene.abundance.txt", "RAP1_IAA_30M_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP1.coverage.gtf", "RAP1_UNINDUCED_REP1.gene.abundance.txt", "RAP1_UNINDUCED_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP2.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP2.coverage.gtf", "RAP1_UNINDUCED_REP2.gene.abundance.txt", "RAP1_UNINDUCED_REP2.transcripts.gtf", "WT_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "WT_REP1.coverage.gtf", "WT_REP1.gene.abundance.txt", "WT_REP1.transcripts.gtf", "WT_REP2.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "WT_REP2.coverage.gtf", "WT_REP2.gene.abundance.txt", @@ -1136,6 +852,8 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ + "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", + 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"minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", + "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", + "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", + "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", + "Coverage Profile Along Genes (High).png:md5,8ec27bae1db26eb468ca35843e5eb557", + "Coverage Profile Along Genes (Low).png:md5,5bed9f6b9e27ad01f60d188f24020c6e", + "Coverage Profile Along Genes (Total).png:md5,bb10036285f9e01ed64048597a25766f", + "Transcript coverage histogram.png:md5,e36d2e717f852cc69f2658e6a901a0ec", "coverage_profile_along_genes_(high).txt:md5,a73462b9ecbd1d2c45d7ca84b5f7925b", "coverage_profile_along_genes_(low).txt:md5,7adc228bc15e344abb7938ea4d35a846", "coverage_profile_along_genes_(total).txt:md5,7adc228bc15e344abb7938ea4d35a846", @@ -1245,17 +1116,38 @@ "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,a2a8e31dbd0ebd0c12f3f968ffd5391b", "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,9ec058d3a4162fd1b4c6175e2106eef4", "WT_REP1.infer_experiment.txt:md5,d55921c0084806cdf49b9bd8653c8e09", - "WT_REP2.infer_experiment.txt:md5,fe87600c55f433ba995fe18bed5cf5f1" + "WT_REP2.infer_experiment.txt:md5,fe87600c55f433ba995fe18bed5cf5f1", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,5dfd0678eefe33f2c45eea45f6262557", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,19a438db88bdb92228e64a0a8350adbd", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,a02dec82f07185700cc237e617ecc809", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,addcf0f6836e0f81184d5ddaa525895f", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,5354c397909a72a25607c550170e2874", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,389b41d0123509f18af9da9bb2e626cd", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,282685569dc501a8769c98c0c2885378", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,daedcbf428f3912587722da1c5db50d1", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,49e5912dedb709344c7a14b5980c1b40", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,7e81ace0a68bfe42482420b7275de195" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T13:41:27.82476" + "timestamp": "2024-09-17T19:40:42.897335" }, "Params: --aligner star_rsem - stub": { "content": [ + 22, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -1295,14 +1187,12 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.1" + "nf-core/rnaseq": "v3.16.0dev" } }, [ "custom", "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw.html", @@ -1334,13 +1224,14 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ - + "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T13:42:16.948827" + "timestamp": "2024-09-17T19:41:35.156352" } } \ No newline at end of file From 6aee372cf9b59b003dbb7e1c0cc49092402e11d0 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 18 Sep 2024 11:21:28 +0200 Subject: [PATCH 052/100] feature counts snapshots --- tests/default.nf.test | 12 +- tests/featurecounts_group_type.nf.test | 20 +- tests/featurecounts_group_type.nf.test.snap | 456 ++++++++------------ tests/hisat2.nf.test | 8 +- tests/kallisto.nf.test | 8 +- tests/min_mapped_reads.nf.test | 8 +- tests/remove_ribo_rna.nf.test | 8 +- tests/salmon.nf.test | 8 +- tests/skip_qc.nf.test | 8 +- tests/skip_trimming.nf.test | 4 +- tests/star_rsem.nf.test | 8 +- 11 files changed, 228 insertions(+), 320 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 829d4471c..681383290 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -12,15 +12,15 @@ nextflow_pipeline { } then { - def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) @@ -39,15 +39,15 @@ nextflow_pipeline { then { - def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index d8da742fc..d9e3d6a9f 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -1,6 +1,6 @@ nextflow_pipeline { - name "Test pipeline without a group type for featureCounts" + name "Test pipeline wjava.lang.String(ithout) a group type for featureCounts" script "../main.nf" test("Params: --featurecounts_group_type false") { @@ -13,15 +13,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } @@ -39,15 +40,16 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def snapshottable_files = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect { it.getName() }, - snapshottable_files + path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_snapshottable ).match() } ) } diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 9e142040a..a770cd9ad 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -1,6 +1,7 @@ { "Params: --featurecounts_group_type false - stub": { "content": [ + 22, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -42,14 +43,12 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.1" + "nf-core/rnaseq": "v3.16.0dev" } }, [ "custom", "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw.html", @@ -81,17 +80,19 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ - + "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T12:49:27.363632" + "timestamp": "2024-09-18T11:14:05.347975" }, "Params: --featurecounts_group_type false": { "content": [ + 188, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -218,7 +219,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.1" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -230,8 +231,6 @@ "WT_REP2.stats.txt", "custom", "out", - "genome_gfp.fasta", - "genome_gfp.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw_1_fastqc.html", @@ -271,40 +270,13 @@ "star_salmon", "multiqc_report.html", "multiqc_report_data", - "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "fastqc-status-check-heatmap-1.txt", - "fastqc-status-check-heatmap.txt", - "fastqc_adapter_content_plot.txt", - "fastqc_overrepresented_sequences_plot-1.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot-1.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot-1.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot-1.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot-1.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot-1.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", - "multiqc_citations.txt", - "multiqc_cutadapt.txt", "multiqc_data.json", "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", - "multiqc_fastqc_fastqc_raw.txt", - "multiqc_fastqc_fastqc_trimmed.txt", "multiqc_general_stats.txt", "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", @@ -319,7 +291,6 @@ "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", - "multiqc_samtools_idxstats.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", @@ -331,16 +302,9 @@ "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", "picard_deduplication.txt", - "picard_histogram.txt", - "picard_histogram_1.txt", - "picard_histogram_2.txt", - "qualimap_gene_coverage_profile_Counts.txt", - "qualimap_gene_coverage_profile_Normalised.txt", "qualimap_genomic_origin.txt", - "qualimap_rnaseq_cov_hist.txt", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", - "rseqc_infer_experiment_plot.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", @@ -356,9 +320,6 @@ "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", "star_alignment_plot.txt", @@ -438,43 +399,21 @@ "png", "cutadapt_filtered_reads_plot-cnt.png", "cutadapt_filtered_reads_plot-pct.png", - "cutadapt_trimmed_sequences_plot_3_Counts.png", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "dupradar-section-plot.png", "fail_strand_check_table.png", - "fastqc-status-check-heatmap-1.png", - "fastqc-status-check-heatmap.png", "fastqc_adapter_content_plot.png", - "fastqc_overrepresented_sequences_plot-1.png", - "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot-1.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot-1.png", "fastqc_per_base_sequence_quality_plot.png", - "fastqc_per_sequence_gc_content_plot-1_Counts.png", - "fastqc_per_sequence_gc_content_plot-1_Percentages.png", - "fastqc_per_sequence_gc_content_plot_Counts.png", - "fastqc_per_sequence_gc_content_plot_Percentages.png", - "fastqc_per_sequence_quality_scores_plot-1.png", - "fastqc_per_sequence_quality_scores_plot.png", - "fastqc_sequence_counts_plot-1-cnt.png", - "fastqc_sequence_counts_plot-1-pct.png", - "fastqc_sequence_counts_plot-cnt.png", - "fastqc_sequence_counts_plot-pct.png", - "fastqc_sequence_duplication_levels_plot-1.png", - "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", "picard_deduplication-cnt.png", "picard_deduplication-pct.png", - "qualimap_gene_coverage_profile_Counts.png", - "qualimap_gene_coverage_profile_Normalised.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", - "rseqc_infer_experiment_plot.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", @@ -486,18 +425,11 @@ "rseqc_junction_saturation_plot_Novel_Junctions.png", "rseqc_read_distribution_plot-cnt.png", "rseqc_read_distribution_plot-pct.png", - "rseqc_read_dups_plot.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png", - "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png", "samtools-stats-dp.png", "samtools_alignment_plot-cnt.png", "samtools_alignment_plot-pct.png", @@ -582,86 +514,55 @@ "salmon", "RAP1_IAA_30M_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", - "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "deseq2_qc", - "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -685,19 +586,13 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", - "tx2gene.tsv", "star_salmon", "RAP1_IAA_30M_REP1", "RAP1_IAA_30M_REP1.markdup.sorted.bam", "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -708,13 +603,8 @@ "RAP1_UNINDUCED_REP1.markdup.sorted.bam", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -725,13 +615,8 @@ "RAP1_UNINDUCED_REP2.markdup.sorted.bam", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -742,13 +627,8 @@ "WT_REP1.markdup.sorted.bam", "WT_REP1.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -759,13 +639,8 @@ "WT_REP2.markdup.sorted.bam", "WT_REP2.markdup.sorted.bam.bai", "aux_info", - "ambig_info.tsv", - "expected_bias.gz", "fld.gz", "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -784,7 +659,6 @@ "WT_REP2.forward.bigWig", "WT_REP2.reverse.bigWig", "deseq2_qc", - "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -804,11 +678,6 @@ "WT_REP1_duprateExpBoxplot.pdf", "WT_REP2_duprateExpBoxplot.pdf", "gene_data", - "RAP1_IAA_30M_REP1_dupMatrix.txt", - "RAP1_UNINDUCED_REP1_dupMatrix.txt", - "RAP1_UNINDUCED_REP2_dupMatrix.txt", - "WT_REP1_dupMatrix.txt", - "WT_REP2_dupMatrix.txt", "histogram", "RAP1_IAA_30M_REP1_expressionHist.pdf", "RAP1_UNINDUCED_REP1_expressionHist.pdf", @@ -816,11 +685,6 @@ "WT_REP1_expressionHist.pdf", "WT_REP2_expressionHist.pdf", "intercepts_slope", - "RAP1_IAA_30M_REP1_intercept_slope.txt", - "RAP1_UNINDUCED_REP1_intercept_slope.txt", - "RAP1_UNINDUCED_REP2_intercept_slope.txt", - "WT_REP1_intercept_slope.txt", - "WT_REP2_intercept_slope.txt", "scatter_plot", "RAP1_IAA_30M_REP1_duprateExpDens.pdf", "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", @@ -831,23 +695,18 @@ "RAP1_IAA_30M_REP1.Log.final.out", "RAP1_IAA_30M_REP1.Log.out", "RAP1_IAA_30M_REP1.Log.progress.out", - "RAP1_IAA_30M_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP1.Log.final.out", "RAP1_UNINDUCED_REP1.Log.out", "RAP1_UNINDUCED_REP1.Log.progress.out", - "RAP1_UNINDUCED_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP2.Log.final.out", "RAP1_UNINDUCED_REP2.Log.out", "RAP1_UNINDUCED_REP2.Log.progress.out", - "RAP1_UNINDUCED_REP2.SJ.out.tab", "WT_REP1.Log.final.out", "WT_REP1.Log.out", "WT_REP1.Log.progress.out", - "WT_REP1.SJ.out.tab", "WT_REP2.Log.final.out", "WT_REP2.Log.out", "WT_REP2.Log.progress.out", - "WT_REP2.SJ.out.tab", "picard_metrics", "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -860,190 +719,90 @@ "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", - "bgfooter.png", - "bgtop.png", - "comment-bright.png", - "comment-close.png", - "comment.png", "doctools.js", - "down-pressed.png", - "down.png", - "file.png", "jquery.js", - "minus.png", - "plus.png", "pygments.css", - "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", - "up-pressed.png", - "up.png", "websupport.js", "images_qualimapReport", - "Coverage Profile Along Genes (High).png", - "Coverage Profile Along Genes (Low).png", - "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", - "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", - "coverage_profile_along_genes_(high).txt", - "coverage_profile_along_genes_(low).txt", - "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "rseqc", "bam_stat", @@ -1053,11 +812,6 @@ "WT_REP1.bam_stat.txt", "WT_REP2.bam_stat.txt", "infer_experiment", - "RAP1_IAA_30M_REP1.infer_experiment.txt", - "RAP1_UNINDUCED_REP1.infer_experiment.txt", - "RAP1_UNINDUCED_REP2.infer_experiment.txt", - "WT_REP1.infer_experiment.txt", - "WT_REP2.infer_experiment.txt", "inner_distance", "pdf", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", @@ -1206,51 +960,30 @@ "WT_REP2.sorted.bam.stats", "stringtie", "RAP1_IAA_30M_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_IAA_30M_REP1.coverage.gtf", "RAP1_IAA_30M_REP1.gene.abundance.txt", "RAP1_IAA_30M_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP1.coverage.gtf", "RAP1_UNINDUCED_REP1.gene.abundance.txt", "RAP1_UNINDUCED_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP2.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP2.coverage.gtf", "RAP1_UNINDUCED_REP2.gene.abundance.txt", "RAP1_UNINDUCED_REP2.transcripts.gtf", "WT_REP1.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "WT_REP1.coverage.gtf", "WT_REP1.gene.abundance.txt", "WT_REP1.transcripts.gtf", "WT_REP2.ballgown", - "e2t.ctab", - "e_data.ctab", - "i2t.ctab", - "i_data.ctab", "t_data.ctab", "WT_REP2.coverage.gtf", "WT_REP2.gene.abundance.txt", "WT_REP2.transcripts.gtf", - "tx2gene.tsv", "trimgalore", "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", @@ -1262,6 +995,8 @@ "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ + "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", + "genome_gfp.gtf:md5,b4776accd1bf7206c7ab0f1d84e4721e", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", @@ -1300,32 +1035,93 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", + "dupradar-section-plot.png:md5,3ae5e5cb161b7abd878d718bc71b41f6", + "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890", + "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84", + "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f", + "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14", + "fastqc_per_sequence_gc_content_plot-1_Counts.png:md5,8a806cec2142f9911502e0a253d83d13", + "fastqc_per_sequence_gc_content_plot-1_Percentages.png:md5,953929d50c8490029880e205e4db7959", + "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16", + "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,eba3abf8bedb2cb20bad90c54e9c8881", + "fastqc_per_sequence_quality_scores_plot-1.png:md5,d2c29cae169f35744500c751b4a7366e", + "fastqc_per_sequence_quality_scores_plot.png:md5,42fd7369a8aca78f620164a9e887c3cb", + "fastqc_sequence_counts_plot-1-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", + "fastqc_sequence_counts_plot-1-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", + "fastqc_sequence_counts_plot-cnt.png:md5,3890d5555f2a39b46b9f6efb14cb91f2", + "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054", + "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", + 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"observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", + "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", @@ -1336,18 +1132,108 @@ "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043", "WT_REP1_intercept_slope.txt:md5,e7fcac6d125a7ba746a5cba4a1e66aef", "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e", + "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", + "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", + "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", + "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204", + "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", + "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + "comment.png:md5,882e40f3d6a16c6ed35659b105251525", + "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", + "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", + "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", + "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", + "Coverage Profile Along Genes (High).png:md5,876c1b88f33bd3e5fe1a41679729573d", + "Coverage Profile Along Genes (Low).png:md5,ee1f2c9cc4dd4867811eda1e68864ab4", + "Coverage Profile Along Genes (Total).png:md5,53747a8f9813744902756ad60638380a", + "Transcript coverage histogram.png:md5,4f9072d4b11216373b59396293803a37", "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8", "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", + "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + "comment.png:md5,882e40f3d6a16c6ed35659b105251525", + "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", + "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", + "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", + "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", + "Coverage Profile Along Genes (High).png:md5,bbf0531018e7fccfc1dfdd1c05715518", + "Coverage Profile Along Genes (Low).png:md5,3c147d9c831d4be98615a22a72fad05d", + "Coverage Profile Along Genes (Total).png:md5,5a8a6db3a8d19a2dcb8f715b11e67c50", + "Transcript coverage histogram.png:md5,488440d7b6d73bcd4567316712e281fe", "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3", "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff", "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", + "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + "comment.png:md5,882e40f3d6a16c6ed35659b105251525", + "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", + "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", + "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", + "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", + "Coverage Profile Along Genes (High).png:md5,5a5d99cc7a1dba3762d67f4aa4adad58", + "Coverage Profile Along Genes (Low).png:md5,b6adc296e9a732aa0495a6da8fa4ed90", + "Coverage Profile Along Genes (Total).png:md5,fcb94fb9c1a51c1db32f884d05929cc8", + "Transcript coverage histogram.png:md5,3aeb52ff3e3752727a370b0d7ceb0518", "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d", "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", + "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + "comment.png:md5,882e40f3d6a16c6ed35659b105251525", + "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", + "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", + "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", + "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", + "Coverage Profile Along Genes (High).png:md5,c974d47996bcc57b99dfaf6903f61f41", + "Coverage Profile Along Genes (Low).png:md5,c8fe631f0580c93adb5be107c6a7a1a3", + "Coverage Profile Along Genes (Total).png:md5,424d245e9f3e626d9e79f51d1b93e946", + "Transcript coverage histogram.png:md5,17404146ad5e0a9bce97ce622e00975e", "coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1", "coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211", "coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211", + "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", + "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", + "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", + "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", + "comment.png:md5,882e40f3d6a16c6ed35659b105251525", + "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", + "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", + "file.png:md5,6587e59c55e626744eb6fc11129d99a7", + "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", + "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", + "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", + "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", + "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", + "Coverage Profile Along Genes (High).png:md5,40edd79c21f3e8d8bbac384156c472d6", + "Coverage Profile Along Genes (Low).png:md5,935c0372259a953a4c99569e9b236ae5", + "Coverage Profile Along Genes (Total).png:md5,34f7a4307be1ea674b7b98eee564d96b", + "Transcript coverage histogram.png:md5,e2abf8a9c62fef57f0be1ca0e01e502d", "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3", "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b", "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b", @@ -1356,6 +1242,26 @@ "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,7d5705880188f9beab1939e08d6b8f40", "WT_REP1.infer_experiment.txt:md5,bf0c137f5fca06e7c40e1984a1acb06d", "WT_REP2.infer_experiment.txt:md5,82e23b329ee60709f343bc2d17d43b14", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,3f149502efe2a9d4bac98b1dd18c15e7", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,a052ab04070e72cc318fb7680b0764e3", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,e82329a443b9ff50a86e42aff91bd704", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,d279003d92f7feef9adb31203f84474a", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,10e2d00f93f9e74f224bd3c1bfbeb29b", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,9aa371befc36478d7720d3ea275e6f4d", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,907ab2e06346df131cbdb929afc005a8", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,b03f3118d1aa58fceadcb3311028e856", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,041edee3193df311f621c09f4991892b", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], @@ -1363,6 +1269,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T12:48:36.937916" + "timestamp": "2024-09-18T11:13:20.643284" } } \ No newline at end of file diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 1c9e6ae59..1d71e59d1 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -13,8 +13,8 @@ nextflow_pipeline { } then { - def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, @@ -40,8 +40,8 @@ nextflow_pipeline { } then { - def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index f81070439..480dcec23 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -15,8 +15,8 @@ nextflow_pipeline { } then { - def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, @@ -44,8 +44,8 @@ nextflow_pipeline { } then { - def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index 7da136cdd..4a741ce29 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -13,8 +13,8 @@ nextflow_pipeline { } then { - def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, @@ -40,8 +40,8 @@ nextflow_pipeline { } then { - def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index 432541d89..bc47a860f 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -13,8 +13,8 @@ nextflow_pipeline { } then { - def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, @@ -40,8 +40,8 @@ nextflow_pipeline { } then { - def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index f543cd932..1638a9fb7 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -15,8 +15,8 @@ nextflow_pipeline { } then { - def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, @@ -44,8 +44,8 @@ nextflow_pipeline { } then { - def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index 1ea1c66ad..6d71e3c3c 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -13,8 +13,8 @@ nextflow_pipeline { } then { - def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, @@ -40,8 +40,8 @@ nextflow_pipeline { } then { - def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index abd2376f6..82dbf43c5 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -13,8 +13,8 @@ nextflow_pipeline { } then { - def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 8f5a82e6b..3210ac3fb 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -13,8 +13,8 @@ nextflow_pipeline { } then { - def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, @@ -40,8 +40,8 @@ nextflow_pipeline { } then { - def path_not_snapshottable = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, From 4d143b5d26962ff1673eb2a9ae1e038ae145a643 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 18 Sep 2024 11:50:18 +0200 Subject: [PATCH 053/100] typo --- tests/featurecounts_group_type.nf.test | 4 ++-- tests/hisat2.nf.test | 4 ++-- tests/kallisto.nf.test | 4 ++-- tests/min_mapped_reads.nf.test | 4 ++-- tests/remove_ribo_rna.nf.test | 4 ++-- tests/salmon.nf.test | 4 ++-- tests/skip_qc.nf.test | 4 ++-- tests/skip_trimming.nf.test | 2 +- tests/star_rsem.nf.test | 4 ++-- 9 files changed, 17 insertions(+), 17 deletions(-) diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index d9e3d6a9f..8d9990960 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -21,7 +21,7 @@ nextflow_pipeline { { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) @@ -48,7 +48,7 @@ nextflow_pipeline { { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 1d71e59d1..a8365dc14 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -21,7 +21,7 @@ nextflow_pipeline { { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) @@ -48,7 +48,7 @@ nextflow_pipeline { { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index 480dcec23..7d6397b76 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -23,7 +23,7 @@ nextflow_pipeline { { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) @@ -52,7 +52,7 @@ nextflow_pipeline { { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index 4a741ce29..20c75605d 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -21,7 +21,7 @@ nextflow_pipeline { { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) @@ -48,7 +48,7 @@ nextflow_pipeline { { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index bc47a860f..52bada874 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -21,7 +21,7 @@ nextflow_pipeline { { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) @@ -48,7 +48,7 @@ nextflow_pipeline { { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index 1638a9fb7..cca7f07aa 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -23,7 +23,7 @@ nextflow_pipeline { { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) @@ -52,7 +52,7 @@ nextflow_pipeline { { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index 6d71e3c3c..dc6f22b31 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -21,7 +21,7 @@ nextflow_pipeline { { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) @@ -48,7 +48,7 @@ nextflow_pipeline { { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index 82dbf43c5..6b013472b 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -21,7 +21,7 @@ nextflow_pipeline { { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 3210ac3fb..f73af622c 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -21,7 +21,7 @@ nextflow_pipeline { { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) @@ -48,7 +48,7 @@ nextflow_pipeline { { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_not_snapshottable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, path_snapshottable ).match() } ) From a3e0328de5deec5d322c312f281ce51d098b2599 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 18 Sep 2024 13:32:20 +0200 Subject: [PATCH 054/100] more snapshots --- tests/hisat2.nf.test.snap | 28 +++++++++++----------- tests/kallisto.nf.test.snap | 36 ++++++++++++++--------------- tests/lib/UTILS.groovy | 24 ++++++++++++++++++- tests/min_mapped_reads.nf.test.snap | 8 +++---- tests/remove_ribo_rna.nf.test.snap | 22 +++++++++--------- tests/star_rsem.nf.test.snap | 36 ++++++++++++++--------------- 6 files changed, 88 insertions(+), 66 deletions(-) diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index a1c47f5c0..e7b482f6e 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -717,6 +717,10 @@ "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "hisat2_pe_plot-cnt.png", + "hisat2_pe_plot-pct.png", + "hisat2_se_plot-cnt.png", + "hisat2_se_plot-pct.png", "picard_deduplication-cnt.png", "picard_deduplication-pct.png", "qualimap_genomic_origin-cnt.png", @@ -775,6 +779,10 @@ "featurecounts_biotype_plot-cnt.svg", "featurecounts_biotype_plot-pct.svg", "general_stats_table.svg", + "hisat2_pe_plot-cnt.svg", + "hisat2_pe_plot-pct.svg", + "hisat2_se_plot-cnt.svg", + "hisat2_se_plot-pct.svg", "picard_deduplication-cnt.svg", "picard_deduplication-pct.svg", "qualimap_gene_coverage_profile_Counts.svg", @@ -928,7 +936,7 @@ "RAP1_UNINDUCED_REP1.hisat2.summary.log:md5,e322e4f7bce12d889a59db517c2ad678", "RAP1_UNINDUCED_REP2.hisat2.summary.log:md5,3f41605b1fbd4d40983915617f8a91f9", "WT_REP1.hisat2.summary.log:md5,50cd2a4fe1f041774c572d09156d4ae8", - "WT_REP2.hisat2.summary.log:md5,e622496abff3ce68afcd1c21a7a1e0df", + "WT_REP2.hisat2.summary.log:md5,5c0d00bfee4ff563521f6458a13f9476", "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", @@ -1094,10 +1102,10 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3625f666cc09d0f07990716aeccd869f", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,6c323b383a6506d124506405b9463d93", - "hisat2_pe_plot-cnt.pdf:md5,5ea21b11336a653206216b189619615d", - "hisat2_pe_plot-pct.pdf:md5,97920acd4cd0ef6c347d1e5196378316", - "hisat2_se_plot-cnt.pdf:md5,162ad273b806726ee519dd85a0ee5521", - "hisat2_se_plot-pct.pdf:md5,6fad42a1c9973d5315bfa6895ef0b8a0", + "hisat2_pe_plot-cnt.pdf:md5,ec0f89f703d3ee1c1d7c59fe712d6467", + "hisat2_pe_plot-pct.pdf:md5,75522edf01667236474caa26c40c4e82", + "hisat2_se_plot-cnt.pdf:md5,15692ca0b4144b4c97094178dcdb39de", + "hisat2_se_plot-pct.pdf:md5,f56040af7a091869364ed1dc8853bc31", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "dupradar-section-plot.png:md5,6074ea2315d296094bd10fad3dcc475b", @@ -1119,10 +1127,6 @@ "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", "featurecounts_biotype_plot-cnt.png:md5,138e00d2fe0af27f2979cf7bdff83b46", "featurecounts_biotype_plot-pct.png:md5,3b7550efe9068f3ada2cc64e311f3338", - "hisat2_pe_plot-cnt.png:md5,1e0841cb32f6aaad84772ff2267b70ad", - "hisat2_pe_plot-pct.png:md5,e201931cd7b31e7227a6273ca1587f56", - "hisat2_se_plot-cnt.png:md5,840937eb5952fa98987a1d2aa8267959", - "hisat2_se_plot-pct.png:md5,51bb5f9ba36dab1ba32fc4e273e865a9", "qualimap_gene_coverage_profile_Counts.png:md5,1aa39028b017760d0b09f1b6f8c1fa3a", "qualimap_gene_coverage_profile_Normalised.png:md5,1cd382a79b89564a006afe431aa3916d", "rseqc_infer_experiment_plot.png:md5,73f5b860029912da9c3f6a887238d251", @@ -1133,10 +1137,6 @@ "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,3bb99f72a15a4159860008beea8c802b", "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,25015f9be4710c4eccc50f30db3bf521", "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,baa90f5ad4d999fc60db30840b72d8c6", - "hisat2_pe_plot-cnt.svg:md5,dae72c87e9e5892ebc1ed5937b737d66", - "hisat2_pe_plot-pct.svg:md5,37d72b7dfc24210dd4f8322f2bb7c801", - "hisat2_se_plot-cnt.svg:md5,785d8da961280cfcd6562bb8b1f8b682", - "hisat2_se_plot-pct.svg:md5,ae694bcf0d5019a534517583507aaaa9", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -1175,6 +1175,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T18:44:49.645101" + "timestamp": "2024-09-18T12:56:26.579349" } } \ No newline at end of file diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index c09795a73..c6319b7aa 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -89,18 +89,28 @@ "kallisto", "RAP1_IAA_30M_REP1", "abundance.h5", + "abundance.tsv", + "kallisto_quant.log", "run_info.json", "RAP1_UNINDUCED_REP1", "abundance.h5", + "abundance.tsv", + "kallisto_quant.log", "run_info.json", "RAP1_UNINDUCED_REP2", "abundance.h5", + "abundance.tsv", + "kallisto_quant.log", "run_info.json", "WT_REP1", "abundance.h5", + "abundance.tsv", + "kallisto_quant.log", "run_info.json", "WT_REP2", "abundance.h5", + "abundance.tsv", + "kallisto_quant.log", "run_info.json", "kallisto.merged.gene_counts.SummarizedExperiment.rds", "kallisto.merged.gene_counts.tsv", @@ -143,6 +153,8 @@ "fastqc_sequence_length_distribution_plot.pdf", "fastqc_top_overrepresented_sequences_table.pdf", "general_stats_table.pdf", + "kallisto_alignment-cnt.pdf", + "kallisto_alignment-pct.pdf", "png", "cutadapt_filtered_reads_plot-cnt.png", "cutadapt_filtered_reads_plot-pct.png", @@ -151,6 +163,8 @@ "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "kallisto_alignment-cnt.png", + "kallisto_alignment-pct.png", "svg", "cutadapt_filtered_reads_plot-cnt.svg", "cutadapt_filtered_reads_plot-pct.svg", @@ -169,6 +183,8 @@ "fastqc_sequence_length_distribution_plot.svg", "fastqc_top_overrepresented_sequences_table.svg", "general_stats_table.svg", + "kallisto_alignment-cnt.svg", + "kallisto_alignment-pct.svg", "pipeline_info", "nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", @@ -184,16 +200,6 @@ [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", - "abundance.tsv:md5,b6ae4ef44f718a789f58dc6451b6eebb", - "kallisto_quant.log:md5,88a4a4c71762af549f1c42308fe80605", - "abundance.tsv:md5,a2c6108c384662f4da8c7b7fe8f27e02", - "kallisto_quant.log:md5,b9c4528ce7c00f5f94e7570507d00a51", - "abundance.tsv:md5,6fd77021287360f5005c90807233ab23", - "kallisto_quant.log:md5,8a9605e9d228c9cbec97b0883d909754", - "abundance.tsv:md5,7b62c5df0930e9f5ebc6e90d6aa600f6", - "kallisto_quant.log:md5,5a7f563172800853c627e8e4f5da6bdc", - "abundance.tsv:md5,6fb211dc8e4fd238ca68d21d6cc83cf5", - "kallisto_quant.log:md5,3447f945ddb20a8eca8aef31b088b8d5", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", @@ -211,8 +217,6 @@ "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "kallisto_alignment-cnt.pdf:md5,a2aa89be43ff1264be51860419219648", - "kallisto_alignment-pct.pdf:md5,41ac1dcf4b41baa598368783eadd92ab", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890", @@ -222,18 +226,14 @@ "fastqc_per_sequence_quality_scores_plot.png:md5,d2c29cae169f35744500c751b4a7366e", "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", - "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", - "kallisto_alignment-cnt.png:md5,989083624e0905b82cbca32f7001a225", - "kallisto_alignment-pct.png:md5,f4de4c6c0fa3ccc83deca870ea2448d2", - "kallisto_alignment-cnt.svg:md5,fc7978ac83c82a3fcc58bb981471a1ee", - "kallisto_alignment-pct.svg:md5,bba0ff4f756a99d943b5b7fff4ab668e" + "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T18:49:01.323612" + "timestamp": "2024-09-18T13:00:14.319235" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index a6b5c512d..9ee624996 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -45,6 +45,7 @@ class UTILS { /cutadapt_trimmed_sequences_.*\.svg/, /dupradar-section-plot\.pdf/, /dupradar-section-plot\.svg/, + /fail_mapped_samples_table.*/, /fail_strand_check_table.*/, /fastqc-status-check-.*\.pdf/, /fastqc-status-check-.*\.svg/, @@ -109,9 +110,16 @@ class UTILS { /general_stats_table\.pdf/, /general_stats_table\.png/, /general_stats_table\.svg/, + /hisat2_pe_plot.*\.png/, + /hisat2_pe_plot.*\.svg/, /hisat2_pe_plot\.txt/, + /hisat2_se_plot.*\.png/, + /hisat2_se_plot.*\.svg/, /junction_saturation_known\.txt/, /junction_saturation_novel\.txt/, + /kallisto_alignment.*.pdf/, + /kallisto_alignment.*.png/, + /kallisto_alignment.*.svg/, /kallisto_alignment\.txt/, /multiqc_data\.json/, /multiqc_dupradar-section-plot\.txt/, @@ -159,6 +167,8 @@ class UTILS { /qualimap_genomic_origin\.txt/, /qualimap_rnaseq_genome_results\.txt/, /rsem_assignment_plot\.txt/, + /rsem_assignment_plot-.*\.pdf/, + /rsem_assignment_plot-.*\.svgf/, /rsem_multimapping_rates\.txt/, /rseqc_bam_stat\.pdf/, /rseqc_bam_stat\.png/, @@ -254,7 +264,7 @@ class UTILS { /samtools_alignment_plot-pct\.png/, /samtools_alignment_plot-pct\.svg/, /samtools_alignment_plot\.txt/, - /sortmerna-detailed-plot\.txt/, + /sortmerna-detailed-plot\.*/, /star_alignment_plot-cnt\.pdf/, /star_alignment_plot-cnt\.png/, /star_alignment_plot-cnt\.svg/, @@ -286,6 +296,8 @@ class UTILS { /deseq2\.size_factors\.RData/, // To exclude from kallisto + /abundance\.tsv/, + /kallisto_quant\.log/, /kallisto\.merged\.gene_counts\.tsv/, /kallisto\.merged\.gene_counts_length_scaled\.tsv/, /kallisto\.merged\.gene_counts_scaled\.tsv/, @@ -380,6 +392,16 @@ class UTILS { /.*\.gene\.abundance\.txt/, /.*\.transcripts\.gtf/, + // To exclude from sortmerna + /.*\.sortmerna\.log/, + + // To exclude log from star rsem + /RAP1_IAA_30M_REP1\.log/, + /RAP1_UNINDUCED_REP1\.log/, + /RAP1_UNINDUCED_REP2\.log/, + /WT_REP1\.log/, + /WT_REP2\.log/, + // To exclude markdup /.*\.markdup\.sorted\.bam/, /.*\.markdup\.sorted\.bam\.bai/, diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 49e7fad77..ceab4f3dd 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -246,6 +246,7 @@ "cutadapt_trimmed_sequences_plot_3_Counts.pdf", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", "dupradar-section-plot.pdf", + "fail_mapped_samples_table.pdf", "fail_strand_check_table.pdf", "fastqc-status-check-heatmap-1.pdf", "fastqc-status-check-heatmap.pdf", @@ -316,6 +317,7 @@ "png", "cutadapt_filtered_reads_plot-cnt.png", "cutadapt_filtered_reads_plot-pct.png", + "fail_mapped_samples_table.png", "fail_strand_check_table.png", "fastqc_adapter_content_plot.png", "fastqc_per_base_n_content_plot-1.png", @@ -361,6 +363,7 @@ "cutadapt_trimmed_sequences_plot_3_Counts.svg", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", "dupradar-section-plot.svg", + "fail_mapped_samples_table.svg", "fail_strand_check_table.svg", "fastqc-status-check-heatmap-1.svg", "fastqc-status-check-heatmap.svg", @@ -852,11 +855,9 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", - "fail_mapped_samples_table.pdf:md5,0d7f9889a09b43eb633b643fd2607442", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "dupradar-section-plot.png:md5,eacbc664cc29a7a59a6aa366b4618582", - "fail_mapped_samples_table.png:md5,e0702273ab75b55895e566cb2945d893", "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890", "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84", "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f", @@ -885,7 +886,6 @@ "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d", "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,a6849cd92ae738441212b681a411614d", "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f", - "fail_mapped_samples_table.svg:md5,e98423866a8f26e67866e81342862256", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -1046,7 +1046,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T18:56:30.086204" + "timestamp": "2024-09-18T13:07:21.624648" }, "Params: --min_mapped_reads 90 - stub": { "content": [ diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 99bc0303a..8075f2513 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -244,7 +244,6 @@ "samtools-flagstat-dp_Read_counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", - "sortmerna-detailed-plot.txt", "star_alignment_plot.txt", "star_summary_table.txt", "multiqc_report_plots", @@ -514,6 +513,11 @@ "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", "sortmerna", + "RAP1_IAA_30M_REP1.sortmerna.log", + "RAP1_UNINDUCED_REP1.sortmerna.log", + "RAP1_UNINDUCED_REP2.sortmerna.log", + "WT_REP1.sortmerna.log", + "WT_REP2.sortmerna.log", "star_salmon", "RAP1_IAA_30M_REP1", "RAP1_IAA_30M_REP1.markdup.sorted.bam", @@ -970,8 +974,9 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,53addd7b78d8ae224920ec9b97489d72", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,97fc7bde65a7efc5ab3af48ef0400c20", - "sortmerna-detailed-plot-cnt.pdf:md5,45068e9eb0457fa236aa842eb20e6579", - "sortmerna-detailed-plot-pct.pdf:md5,141dbadd12bdfe5e424089f547ae9241", + "sortmerna-detailed-plot.txt:md5,245e3f5575f2886943c833a4d26e5b8c", + "sortmerna-detailed-plot-cnt.pdf:md5,c99ee88cfbaa772aabd2c13e0d41d774", + "sortmerna-detailed-plot-pct.pdf:md5,956d8f55067b3e1bfa5b86797d701e6e", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "dupradar-section-plot.png:md5,62ee84d3b32bdbfb9766fa970680f92c", @@ -1005,8 +1010,8 @@ "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,1a029e5d23f82d537470363a065b644a", "sortmerna-detailed-plot-cnt.png:md5,3875997f21c98e8906cd182d959e0020", "sortmerna-detailed-plot-pct.png:md5,971398875e5cbd50313b6fee7eeb302c", - "sortmerna-detailed-plot-cnt.svg:md5,4cf8f33f9c4b5fa32ca5fa0f1da34521", - "sortmerna-detailed-plot-pct.svg:md5,9e3e7732d400e8fed44bd9b5442f7f9e", + "sortmerna-detailed-plot-cnt.svg:md5,46aca790cbf000df1d77df814dc9f0a1", + "sortmerna-detailed-plot-pct.svg:md5,3be76f5e789415280b17689f90869fac", "ambig_info.tsv:md5,25ced9693254994a7878241225baabb6", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -1039,11 +1044,6 @@ "lib_format_counts.json:md5,e6e3d7746e9abee6a0e097ae0ee1781a", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", - "RAP1_IAA_30M_REP1.sortmerna.log:md5,b178353fbd4dbc526ddeb8cd62692898", - "RAP1_UNINDUCED_REP1.sortmerna.log:md5,9fc2dc3709b7b316a7c1c4b60d02b192", - "RAP1_UNINDUCED_REP2.sortmerna.log:md5,3ed13bf8ec109ab8e8da6224d0dd29c0", - "WT_REP1.sortmerna.log:md5,5b4548062572db0b14ab05c66e2914bb", - "WT_REP2.sortmerna.log:md5,976d7a76f560c3107c670396b93b9fbb", "ambig_info.tsv:md5,6cd02367152bb2dd59a6f1f70df2d7f8", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -1232,7 +1232,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T19:09:08.723809" + "timestamp": "2024-09-18T13:21:54.460278" }, "Params: --remove_ribo_rna - stub": { "content": [ diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 14112208c..6bf284f43 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -274,6 +274,8 @@ "qualimap_gene_coverage_profile_Normalised.pdf", "qualimap_genomic_origin-cnt.pdf", "qualimap_genomic_origin-pct.pdf", + "rsem_assignment_plot-cnt.pdf", + "rsem_assignment_plot-pct.pdf", "rseqc_bam_stat.pdf", "rseqc_infer_experiment_plot.pdf", "rseqc_inner_distance_plot_Counts.pdf", @@ -576,6 +578,11 @@ "WT_REP1.featureCounts.txt.summary", "WT_REP2.featureCounts.txt.summary", "log", + "RAP1_IAA_30M_REP1.log", + "RAP1_UNINDUCED_REP1.log", + "RAP1_UNINDUCED_REP2.log", + "WT_REP1.log", + "WT_REP2.log", "picard_metrics", "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -899,11 +906,9 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3e67e07b5c978fa363965e8e90356eef", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,a83e44c5a22e014d377c41419175784c", - "rsem_assignment_plot-cnt.pdf:md5,b1105b7b976994475f6e85adff4b78c5", - "rsem_assignment_plot-pct.pdf:md5,11f4d45b61f1bf7ea77fbb618cfa2737", - "rsem_multimapping_rates.pdf:md5,b23150fbb594836f35d67b65db06a3de", - "star_rsem_deseq2_clustering-plot.pdf:md5,423a5a10d0b1a24f250273b10f22eb8c", - "star_rsem_deseq2_pca-plot.pdf:md5,91dd48d31c4d6fe980710b4f0aec6e5b", + "rsem_multimapping_rates.pdf:md5,4e230eba3c947fda36063d63bd106b4b", + "star_rsem_deseq2_clustering-plot.pdf:md5,9f24a6a38979abb3fe7214b9f9d637da", + "star_rsem_deseq2_pca-plot.pdf:md5,673524df75bd25374f1cc93b47cd1d93", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "dupradar-section-plot.png:md5,f76a34d2eb6f2351729d79efc1434ee8", @@ -927,8 +932,8 @@ "featurecounts_biotype_plot-pct.png:md5,1921c3931d871f8326a6a6c5c8278815", "qualimap_gene_coverage_profile_Counts.png:md5,04a262d5af169d6d771e48555adab37e", "qualimap_gene_coverage_profile_Normalised.png:md5,3bddc4f2a7d462996628e33daf490247", - "rsem_assignment_plot-cnt.png:md5,dbd1c9db455302b778b5abd4fb3f2518", - "rsem_assignment_plot-pct.png:md5,7f5c5102f019ef24489335aa8f08f708", + "rsem_assignment_plot-cnt.png:md5,15fd495eeee0d791d8fe663c9a981b6a", + "rsem_assignment_plot-pct.png:md5,e38d64af2acd404fcdb72a55a6dd1986", "rsem_multimapping_rates.png:md5,e93d35b86e1be681eae9b6ad19e12350", "rseqc_infer_experiment_plot.png:md5,1a3a792e9a6e0c0f93c082594b24e566", "rseqc_read_dups_plot.png:md5,b79c01ce4697ebb7e0ebb4a3da5b44f7", @@ -940,11 +945,11 @@ "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,5d2286a4f77000c199ed22517338da4a", "star_rsem_deseq2_clustering-plot.png:md5,6e096e2872cb6377346dc2b02c1eefc7", "star_rsem_deseq2_pca-plot.png:md5,baced09efc64db394115fa01683e206d", - "rsem_assignment_plot-cnt.svg:md5,9d357747ae789f7da5909baf35377efb", - "rsem_assignment_plot-pct.svg:md5,97d944dd054d90e6378f8f48b5b098ed", - "rsem_multimapping_rates.svg:md5,9bed82e20eeaf247ab7fb3db5ea186e6", - "star_rsem_deseq2_clustering-plot.svg:md5,6c99957b57fc6941ad21ef66d9a4b9d4", - "star_rsem_deseq2_pca-plot.svg:md5,9a2a59fdeafc8cd5f7f8346d04a76545", + "rsem_assignment_plot-cnt.svg:md5,5ecdbb29a5de8609a414e90f3154582d", + "rsem_assignment_plot-pct.svg:md5,73f7ced521db5522230b349a05def6f6", + "rsem_multimapping_rates.svg:md5,8a7303b79af32506ba6165e8722fcec5", + "star_rsem_deseq2_clustering-plot.svg:md5,3e95856c1c1eaa02b7ddd99b44230f1a", + "star_rsem_deseq2_pca-plot.svg:md5,3a6c169e6499931d22df1a2b74973a08", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -1003,11 +1008,6 @@ "WT_REP2.biotype_counts_mqc.tsv:md5,d4957c0197636b68d27fbd60d388bba1", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", "WT_REP2.featureCounts.txt:md5,152d2f26df56a88fe4b27c742d8f7447", - "RAP1_IAA_30M_REP1.log:md5,9ae83e17609989ecd028de9c48631083", - "RAP1_UNINDUCED_REP1.log:md5,4ba1411eaaa133b8b175a77c80b93446", - "RAP1_UNINDUCED_REP2.log:md5,ceb728b91240d874840bbf67bb9ab32d", - "WT_REP1.log:md5,4f2a1c6ebb27f0368526d547191d3676", - "WT_REP2.log:md5,bf30cb12c1676fa72b6cb8fa70936b1a", "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", @@ -1143,7 +1143,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T19:40:42.897335" + "timestamp": "2024-09-18T13:29:39.499413" }, "Params: --aligner star_rsem - stub": { "content": [ From 4811e91a868a9da51ed3c716054af7b34cae68b7 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 18 Sep 2024 14:28:24 +0200 Subject: [PATCH 055/100] more snapshots --- tests/hisat2.nf.test.snap | 22 ++++++------- tests/lib/UTILS.groovy | 52 ++++++++++++------------------ tests/remove_ribo_rna.nf.test.snap | 38 +++++++++++----------- tests/star_rsem.nf.test.snap | 32 +++++++++--------- 4 files changed, 67 insertions(+), 77 deletions(-) diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index e7b482f6e..3b5622a35 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -604,11 +604,6 @@ "multiqc_rseqc_junction_annotation.txt", "multiqc_rseqc_read_distribution.txt", "multiqc_salmon.txt", - "multiqc_salmon_deseq2_clustering-plot.txt", - "multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", "multiqc_samtools_stats.txt", @@ -936,7 +931,7 @@ "RAP1_UNINDUCED_REP1.hisat2.summary.log:md5,e322e4f7bce12d889a59db517c2ad678", "RAP1_UNINDUCED_REP2.hisat2.summary.log:md5,3f41605b1fbd4d40983915617f8a91f9", "WT_REP1.hisat2.summary.log:md5,50cd2a4fe1f041774c572d09156d4ae8", - "WT_REP2.hisat2.summary.log:md5,5c0d00bfee4ff563521f6458a13f9476", + "WT_REP2.hisat2.summary.log:md5,e622496abff3ce68afcd1c21a7a1e0df", "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", @@ -1091,6 +1086,11 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,d35ad008181f0f7be84d5770d17a3a65", + "multiqc_salmon_deseq2_clustering-plot.txt:md5,c39fd219828df33259e48aadcdd1997c", + "multiqc_salmon_deseq2_clustering-plot_1.txt:md5,6ccabfcdd11d36e140a7d6615c73ae85", + "multiqc_salmon_deseq2_clustering-plot_2.txt:md5,792ce8a58aefbbd10c0f182fcbc37c7a", + "multiqc_salmon_deseq2_clustering-plot_3.txt:md5,3080d13dee6e437084f27937296ede8a", + "multiqc_salmon_deseq2_clustering-plot_4.txt:md5,c750d2fa8d6dc8a2370335a71d2fa637", "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1102,10 +1102,10 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3625f666cc09d0f07990716aeccd869f", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,6c323b383a6506d124506405b9463d93", - "hisat2_pe_plot-cnt.pdf:md5,ec0f89f703d3ee1c1d7c59fe712d6467", - "hisat2_pe_plot-pct.pdf:md5,75522edf01667236474caa26c40c4e82", - "hisat2_se_plot-cnt.pdf:md5,15692ca0b4144b4c97094178dcdb39de", - "hisat2_se_plot-pct.pdf:md5,f56040af7a091869364ed1dc8853bc31", + "hisat2_pe_plot-cnt.pdf:md5,597b9758f57712f66956d1065f72f68c", + "hisat2_pe_plot-pct.pdf:md5,6baadc07e1d4b51a872fdf288d3a5dcd", + "hisat2_se_plot-cnt.pdf:md5,ad78c3a76df184a45d0b9f905ed979d0", + "hisat2_se_plot-pct.pdf:md5,60a38be9382dbf103bb0832c2f1bca6c", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "dupradar-section-plot.png:md5,6074ea2315d296094bd10fad3dcc475b", @@ -1175,6 +1175,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-18T12:56:26.579349" + "timestamp": "2024-09-18T14:05:59.799519" } } \ No newline at end of file diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index 9ee624996..f54b96da6 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -110,11 +110,9 @@ class UTILS { /general_stats_table\.pdf/, /general_stats_table\.png/, /general_stats_table\.svg/, - /hisat2_pe_plot.*\.png/, - /hisat2_pe_plot.*\.svg/, + /hisat2_(pe|se)_plot-(cnt|pct)\.(png|svg)/, /hisat2_pe_plot\.txt/, - /hisat2_se_plot.*\.png/, - /hisat2_se_plot.*\.svg/, + /hisat2_se_plot.*\.(png|svg)/, /junction_saturation_known\.txt/, /junction_saturation_novel\.txt/, /kallisto_alignment.*.pdf/, @@ -135,8 +133,8 @@ class UTILS { /multiqc_rseqc_junction_annotation\.txt/, /multiqc_rseqc_read_distribution\.txt/, /multiqc_salmon\.txt/, - /multiqc_salmon_deseq2_clustering-plot\.txt/, - /multiqc_salmon_deseq2_clustering-plot_.*\.txt/, + /(star_rsem|multiqc_salmon)_deseq2_clustering-plot-\.txt/, + /(star_rsem|multiqc_salmon)_deseq2_clustering_-lot_-.*\.txt/, /multiqc_salmon_deseq2_pca-plot\.txt/, /multiqc_samtools_flagstat\.txt/, /multiqc_samtools_stats\.txt/, @@ -144,8 +142,8 @@ class UTILS { /multiqc_sortmerna\.txt/, /multiqc_sources\.txt/, /multiqc_star\.txt/, - /multiqc_star_salmon_deseq2_clustering-plot\.txt/, - /multiqc_star_salmon_deseq2_clustering-plot_.*\.txt/, + /(star_rsem|multiqc_star_salmon)_deseq2_clustering-plot-\.txt/, + /(star_rsem|multiqc_star_salmon)_deseq2_clustering_-lot_-.*\.txt/, /multiqc_star_salmon_deseq2_pca-plot\.txt/, /picard_deduplication-cnt\.pdf/, /picard_deduplication-cnt\.png/, @@ -167,9 +165,8 @@ class UTILS { /qualimap_genomic_origin\.txt/, /qualimap_rnaseq_genome_results\.txt/, /rsem_assignment_plot\.txt/, - /rsem_assignment_plot-.*\.pdf/, - /rsem_assignment_plot-.*\.svgf/, - /rsem_multimapping_rates\.txt/, + /rsem_assignment_plot-(cnt|pct)\.(pdf|svg)/, + /rsem_multimapping_rates\.(pdf|svg|txt)/, /rseqc_bam_stat\.pdf/, /rseqc_bam_stat\.png/, /rseqc_bam_stat\.svg/, @@ -223,12 +220,12 @@ class UTILS { /rseqc_read_dups_plot\.pdf/, /rseqc_read_dups_plot\.svg/, /rseqc_read_dups_plot\.txt/, - /salmon_deseq2_clustering-plot\.pdf/, - /salmon_deseq2_clustering-plot\.png/, - /salmon_deseq2_clustering-plot\.svg/, - /salmon_deseq2_pca-plot\.pdf/, - /salmon_deseq2_pca-plot\.png/, - /salmon_deseq2_pca-plot\.svg/, + /(salmon|star_rsem)_deseq2_(clustering|pca)-plot\.pdf/, + /(salmon|star_rsem)_deseq2_(clustering|pca)-plot\.png/, + /(salmon|star_rsem)_deseq2_(clustering|pca)-plot\.svg/, + /(salmon|star_rsem)_deseq2_(pca|pca)-plot\.pdf/, + /(salmon|star_rsem)_deseq2_(pca|pca)-plot\.png/, + /(salmon|star_rsem)_deseq2_(pca|pca)-plot\.svg/, /salmon_plot\.pdf/, /salmon_plot\.png/, /salmon_plot\.svg/, @@ -264,7 +261,7 @@ class UTILS { /samtools_alignment_plot-pct\.png/, /samtools_alignment_plot-pct\.svg/, /samtools_alignment_plot\.txt/, - /sortmerna-detailed-plot\.*/, + /sortmerna-detailed-plot-(cnt|pct)\.(pdf|svg)/, /star_alignment_plot-cnt\.pdf/, /star_alignment_plot-cnt\.png/, /star_alignment_plot-cnt\.svg/, @@ -272,9 +269,7 @@ class UTILS { /star_alignment_plot-pct\.png/, /star_alignment_plot-pct\.svg/, /star_alignment_plot\.txt/, - /star_salmon_deseq2_clustering-plot\.pdf/, - /star_salmon_deseq2_clustering-plot\.png/, - /star_salmon_deseq2_clustering-plot\.svg/, + /(star_rsem|star_salmon)_deseq2_(clustering|pca)-plot-\.(pdf|png|svg)/, /star_salmon_deseq2_pca-plot\.pdf/, /star_salmon_deseq2_pca-plot\.png/, /star_salmon_deseq2_pca-plot\.svg/, @@ -379,12 +374,10 @@ class UTILS { /.*\.bam_stat\.txt/, // To exclude from samtools stats - /.*\.markdup\.sorted\.bam\.flagstat/, - /.*\.markdup\.sorted\.bam\.idxstats/, - /.*\.markdup\.sorted\.bam\.stats/, - /.*\.sorted\.bam\.flagstat/, - /.*\.sorted\.bam\.idxstats/, - /.*\.sorted\.bam\.stats/, + /.*\.sorted\.bam\.(flagstat|idxstats|stats)/, + + // To exclude from hisat2 + /.*hisat2\.summary/, // To exclude from stringtie /t_data\.ctab/, @@ -407,10 +400,7 @@ class UTILS { /.*\.markdup\.sorted\.bam\.bai/, // To exclude trimgalore - /.*\.fastq\.gz_trimming_report\.txt/, - - // To exclude params files with timestamps - /params_\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}\.json/ + /.*\.fastq\.gz_trimming_report\.txt/ ] } diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 8075f2513..40aa30e4f 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -205,11 +205,6 @@ "multiqc_rseqc_junction_annotation.txt", "multiqc_rseqc_read_distribution.txt", "multiqc_salmon.txt", - "multiqc_salmon_deseq2_clustering-plot.txt", - "multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", "multiqc_samtools_stats.txt", @@ -217,11 +212,6 @@ "multiqc_sortmerna.txt", "multiqc_sources.txt", "multiqc_star.txt", - "multiqc_star_salmon_deseq2_clustering-plot.txt", - "multiqc_star_salmon_deseq2_clustering-plot_1.txt", - "multiqc_star_salmon_deseq2_clustering-plot_2.txt", - "multiqc_star_salmon_deseq2_clustering-plot_3.txt", - "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", "picard_deduplication.txt", "qualimap_genomic_origin.txt", @@ -315,9 +305,10 @@ "samtools-stats-dp.pdf", "samtools_alignment_plot-cnt.pdf", "samtools_alignment_plot-pct.pdf", + "sortmerna-detailed-plot-cnt.pdf", + "sortmerna-detailed-plot-pct.pdf", "star_alignment_plot-cnt.pdf", "star_alignment_plot-pct.pdf", - "star_salmon_deseq2_clustering-plot.pdf", "star_salmon_deseq2_pca-plot.pdf", "star_summary_table.pdf", "png", @@ -359,7 +350,6 @@ "samtools_alignment_plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", - "star_salmon_deseq2_clustering-plot.png", "star_salmon_deseq2_pca-plot.png", "star_summary_table.png", "svg", @@ -430,9 +420,10 @@ "samtools-stats-dp.svg", "samtools_alignment_plot-cnt.svg", "samtools_alignment_plot-pct.svg", + "sortmerna-detailed-plot-cnt.svg", + "sortmerna-detailed-plot-pct.svg", "star_alignment_plot-cnt.svg", "star_alignment_plot-pct.svg", - "star_salmon_deseq2_clustering-plot.svg", "star_salmon_deseq2_pca-plot.svg", "star_summary_table.svg", "pipeline_info", @@ -963,7 +954,17 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,54f0eef4ab0ecf6a03505b18752b43cd", + "multiqc_salmon_deseq2_clustering-plot.txt:md5,b84f4797086941a5014d88dc46115832", + "multiqc_salmon_deseq2_clustering-plot_1.txt:md5,7494c2892cc5b058da9e2296f7be5a8c", + "multiqc_salmon_deseq2_clustering-plot_2.txt:md5,4b6e40f595eb28ceaadf43ffe187b752", + "multiqc_salmon_deseq2_clustering-plot_3.txt:md5,d0d2a9e2bf3d4e81fef9b2450e5e29b8", + "multiqc_salmon_deseq2_clustering-plot_4.txt:md5,0ab6a0bc900cb8bae5aa280e2d13397a", "multiqc_samtools_idxstats.txt:md5,413ba06f3d8e4ab0dbde8ef8952c4b32", + "multiqc_star_salmon_deseq2_clustering-plot.txt:md5,99d097781c6761b6894e6bcc7999e1ba", + "multiqc_star_salmon_deseq2_clustering-plot_1.txt:md5,88bcc02233b2df2876678d186df8d32a", + "multiqc_star_salmon_deseq2_clustering-plot_2.txt:md5,8673d08e63e16dc7993f99f15c8377e1", + "multiqc_star_salmon_deseq2_clustering-plot_3.txt:md5,b65a05ab4904d2992d3bf664ad0e82f1", + "multiqc_star_salmon_deseq2_clustering-plot_4.txt:md5,5c77c5fefc953051de1fc1e6d8377cf2", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -974,9 +975,8 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,53addd7b78d8ae224920ec9b97489d72", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,97fc7bde65a7efc5ab3af48ef0400c20", - "sortmerna-detailed-plot.txt:md5,245e3f5575f2886943c833a4d26e5b8c", - "sortmerna-detailed-plot-cnt.pdf:md5,c99ee88cfbaa772aabd2c13e0d41d774", - "sortmerna-detailed-plot-pct.pdf:md5,956d8f55067b3e1bfa5b86797d701e6e", + "sortmerna-detailed-plot.txt:md5,b93dadb4ca77c6af68ef2c00a8626f17", + "star_salmon_deseq2_clustering-plot.pdf:md5,1a1cfea5266d1857da02f0e7c9e062bb", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "dupradar-section-plot.png:md5,62ee84d3b32bdbfb9766fa970680f92c", @@ -1010,8 +1010,8 @@ "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,1a029e5d23f82d537470363a065b644a", "sortmerna-detailed-plot-cnt.png:md5,3875997f21c98e8906cd182d959e0020", "sortmerna-detailed-plot-pct.png:md5,971398875e5cbd50313b6fee7eeb302c", - "sortmerna-detailed-plot-cnt.svg:md5,46aca790cbf000df1d77df814dc9f0a1", - "sortmerna-detailed-plot-pct.svg:md5,3be76f5e789415280b17689f90869fac", + "star_salmon_deseq2_clustering-plot.png:md5,86ae8d342372b9fe5c8ad3108890606a", + "star_salmon_deseq2_clustering-plot.svg:md5,d414f141d8af259802fb059c8a376ac5", "ambig_info.tsv:md5,25ced9693254994a7878241225baabb6", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -1232,7 +1232,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-18T13:21:54.460278" + "timestamp": "2024-09-18T14:19:29.058683" }, "Params: --remove_ribo_rna - stub": { "content": [ diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 6bf284f43..6e11a8df9 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -200,11 +200,6 @@ "multiqc_rseqc_junction_annotation.txt", "multiqc_rseqc_read_distribution.txt", "multiqc_salmon.txt", - "multiqc_salmon_deseq2_clustering-plot.txt", - "multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", "multiqc_samtools_stats.txt", @@ -276,6 +271,7 @@ "qualimap_genomic_origin-pct.pdf", "rsem_assignment_plot-cnt.pdf", "rsem_assignment_plot-pct.pdf", + "rsem_multimapping_rates.pdf", "rseqc_bam_stat.pdf", "rseqc_infer_experiment_plot.pdf", "rseqc_inner_distance_plot_Counts.pdf", @@ -304,6 +300,8 @@ "samtools-stats-dp.pdf", "samtools_alignment_plot-cnt.pdf", "samtools_alignment_plot-pct.pdf", + "star_rsem_deseq2_clustering-plot.pdf", + "star_rsem_deseq2_pca-plot.pdf", "png", "cutadapt_filtered_reads_plot-cnt.png", "cutadapt_filtered_reads_plot-pct.png", @@ -341,6 +339,8 @@ "samtools-stats-dp.png", "samtools_alignment_plot-cnt.png", "samtools_alignment_plot-pct.png", + "star_rsem_deseq2_clustering-plot.png", + "star_rsem_deseq2_pca-plot.png", "svg", "cutadapt_filtered_reads_plot-cnt.svg", "cutadapt_filtered_reads_plot-pct.svg", @@ -381,6 +381,9 @@ "qualimap_gene_coverage_profile_Normalised.svg", "qualimap_genomic_origin-cnt.svg", "qualimap_genomic_origin-pct.svg", + "rsem_assignment_plot-cnt.svg", + "rsem_assignment_plot-pct.svg", + "rsem_multimapping_rates.svg", "rseqc_bam_stat.svg", "rseqc_infer_experiment_plot.svg", "rseqc_inner_distance_plot_Counts.svg", @@ -409,6 +412,8 @@ "samtools-stats-dp.svg", "samtools_alignment_plot-cnt.svg", "samtools_alignment_plot-pct.svg", + "star_rsem_deseq2_clustering-plot.svg", + "star_rsem_deseq2_pca-plot.svg", "pipeline_info", "nf_core_rnaseq_software_mqc_versions.yml", "salmon", @@ -889,6 +894,11 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,27bb37d346e8f0960c882a3676e219e8", + "multiqc_salmon_deseq2_clustering-plot.txt:md5,f5d583266ecc0d0eaddb7a8362405164", + "multiqc_salmon_deseq2_clustering-plot_1.txt:md5,2a1097fe03e12542dd198ed805ba108a", + "multiqc_salmon_deseq2_clustering-plot_2.txt:md5,5f7195951fd89a62b45d16991d0c83d0", + "multiqc_salmon_deseq2_clustering-plot_3.txt:md5,eab5db39f3ee13163329402a87cafd21", + "multiqc_salmon_deseq2_clustering-plot_4.txt:md5,c3287dd65316b9afb54f2c3f6931fa51", "multiqc_samtools_idxstats.txt:md5,1cbc64fc9713831a6f45effc0cfe6a39", "multiqc_star_rsem_deseq2_clustering-plot.txt:md5,62bd581d9ea4cc3fb2dbddeb82238ed2", "multiqc_star_rsem_deseq2_clustering-plot_1.txt:md5,acd14c14552684ef5783a490de0bc704", @@ -906,9 +916,6 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3e67e07b5c978fa363965e8e90356eef", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,a83e44c5a22e014d377c41419175784c", - "rsem_multimapping_rates.pdf:md5,4e230eba3c947fda36063d63bd106b4b", - "star_rsem_deseq2_clustering-plot.pdf:md5,9f24a6a38979abb3fe7214b9f9d637da", - "star_rsem_deseq2_pca-plot.pdf:md5,673524df75bd25374f1cc93b47cd1d93", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "dupradar-section-plot.png:md5,f76a34d2eb6f2351729d79efc1434ee8", @@ -943,13 +950,6 @@ "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,10d7c1023bcf922ac45e653a58ee13c8", "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,2edc4372d981aacfceb4f16da598d63a", "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,5d2286a4f77000c199ed22517338da4a", - "star_rsem_deseq2_clustering-plot.png:md5,6e096e2872cb6377346dc2b02c1eefc7", - "star_rsem_deseq2_pca-plot.png:md5,baced09efc64db394115fa01683e206d", - "rsem_assignment_plot-cnt.svg:md5,5ecdbb29a5de8609a414e90f3154582d", - "rsem_assignment_plot-pct.svg:md5,73f7ced521db5522230b349a05def6f6", - "rsem_multimapping_rates.svg:md5,8a7303b79af32506ba6165e8722fcec5", - "star_rsem_deseq2_clustering-plot.svg:md5,3e95856c1c1eaa02b7ddd99b44230f1a", - "star_rsem_deseq2_pca-plot.svg:md5,3a6c169e6499931d22df1a2b74973a08", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -1143,7 +1143,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-18T13:29:39.499413" + "timestamp": "2024-09-18T14:27:07.132344" }, "Params: --aligner star_rsem - stub": { "content": [ From 30d629b03fc26ad805af38133e68da04965a5351 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 18 Sep 2024 15:12:56 +0200 Subject: [PATCH 056/100] update snapshots --- tests/hisat2.nf.test.snap | 20 ++++++++++---------- tests/lib/UTILS.groovy | 11 ++++------- tests/star_rsem.nf.test.snap | 16 ++++++++-------- 3 files changed, 22 insertions(+), 25 deletions(-) diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 3b5622a35..c6dcc97bd 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -604,6 +604,11 @@ "multiqc_rseqc_junction_annotation.txt", "multiqc_rseqc_read_distribution.txt", "multiqc_salmon.txt", + "multiqc_salmon_deseq2_clustering-plot.txt", + "multiqc_salmon_deseq2_clustering-plot_1.txt", + "multiqc_salmon_deseq2_clustering-plot_2.txt", + "multiqc_salmon_deseq2_clustering-plot_3.txt", + "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", "multiqc_samtools_stats.txt", @@ -665,6 +670,10 @@ "featurecounts_biotype_plot-cnt.pdf", "featurecounts_biotype_plot-pct.pdf", "general_stats_table.pdf", + "hisat2_pe_plot-cnt.pdf", + "hisat2_pe_plot-pct.pdf", + "hisat2_se_plot-cnt.pdf", + "hisat2_se_plot-pct.pdf", "picard_deduplication-cnt.pdf", "picard_deduplication-pct.pdf", "qualimap_gene_coverage_profile_Counts.pdf", @@ -1086,11 +1095,6 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,d35ad008181f0f7be84d5770d17a3a65", - "multiqc_salmon_deseq2_clustering-plot.txt:md5,c39fd219828df33259e48aadcdd1997c", - "multiqc_salmon_deseq2_clustering-plot_1.txt:md5,6ccabfcdd11d36e140a7d6615c73ae85", - "multiqc_salmon_deseq2_clustering-plot_2.txt:md5,792ce8a58aefbbd10c0f182fcbc37c7a", - "multiqc_salmon_deseq2_clustering-plot_3.txt:md5,3080d13dee6e437084f27937296ede8a", - "multiqc_salmon_deseq2_clustering-plot_4.txt:md5,c750d2fa8d6dc8a2370335a71d2fa637", "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1102,10 +1106,6 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3625f666cc09d0f07990716aeccd869f", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,6c323b383a6506d124506405b9463d93", - "hisat2_pe_plot-cnt.pdf:md5,597b9758f57712f66956d1065f72f68c", - "hisat2_pe_plot-pct.pdf:md5,6baadc07e1d4b51a872fdf288d3a5dcd", - "hisat2_se_plot-cnt.pdf:md5,ad78c3a76df184a45d0b9f905ed979d0", - "hisat2_se_plot-pct.pdf:md5,60a38be9382dbf103bb0832c2f1bca6c", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "dupradar-section-plot.png:md5,6074ea2315d296094bd10fad3dcc475b", @@ -1175,6 +1175,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-18T14:05:59.799519" + "timestamp": "2024-09-18T15:04:27.247526" } } \ No newline at end of file diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index f54b96da6..41d7f991b 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -110,7 +110,7 @@ class UTILS { /general_stats_table\.pdf/, /general_stats_table\.png/, /general_stats_table\.svg/, - /hisat2_(pe|se)_plot-(cnt|pct)\.(png|svg)/, + /hisat2_(pe|se)_plot-(cnt|pct)\.(pdf|png|svg)/, /hisat2_pe_plot\.txt/, /hisat2_se_plot.*\.(png|svg)/, /junction_saturation_known\.txt/, @@ -133,17 +133,14 @@ class UTILS { /multiqc_rseqc_junction_annotation\.txt/, /multiqc_rseqc_read_distribution\.txt/, /multiqc_salmon\.txt/, - /(star_rsem|multiqc_salmon)_deseq2_clustering-plot-\.txt/, - /(star_rsem|multiqc_salmon)_deseq2_clustering_-lot_-.*\.txt/, - /multiqc_salmon_deseq2_pca-plot\.txt/, + /(star_rsem|multiqc_salmon|multiqc_star_salmon)_deseq2_clustering-plot.*\.(pdf|png|txt)/, + /multiqc_salmon_deseq2_pca-plot.*\.txt/, /multiqc_samtools_flagstat\.txt/, /multiqc_samtools_stats\.txt/, /multiqc_software_versions\.txt/, /multiqc_sortmerna\.txt/, /multiqc_sources\.txt/, /multiqc_star\.txt/, - /(star_rsem|multiqc_star_salmon)_deseq2_clustering-plot-\.txt/, - /(star_rsem|multiqc_star_salmon)_deseq2_clustering_-lot_-.*\.txt/, /multiqc_star_salmon_deseq2_pca-plot\.txt/, /picard_deduplication-cnt\.pdf/, /picard_deduplication-cnt\.png/, @@ -165,7 +162,7 @@ class UTILS { /qualimap_genomic_origin\.txt/, /qualimap_rnaseq_genome_results\.txt/, /rsem_assignment_plot\.txt/, - /rsem_assignment_plot-(cnt|pct)\.(pdf|svg)/, + /rsem_assignment_plot-(cnt|pct)\.(pdf|png|svg)/, /rsem_multimapping_rates\.(pdf|svg|txt)/, /rseqc_bam_stat\.pdf/, /rseqc_bam_stat\.png/, diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 6e11a8df9..5cd9614f8 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -200,6 +200,11 @@ "multiqc_rseqc_junction_annotation.txt", "multiqc_rseqc_read_distribution.txt", "multiqc_salmon.txt", + "multiqc_salmon_deseq2_clustering-plot.txt", + "multiqc_salmon_deseq2_clustering-plot_1.txt", + "multiqc_salmon_deseq2_clustering-plot_2.txt", + "multiqc_salmon_deseq2_clustering-plot_3.txt", + "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", "multiqc_samtools_stats.txt", @@ -319,6 +324,8 @@ "picard_deduplication-pct.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", + "rsem_assignment_plot-cnt.png", + "rsem_assignment_plot-pct.png", "rseqc_bam_stat.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", @@ -894,11 +901,6 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,27bb37d346e8f0960c882a3676e219e8", - "multiqc_salmon_deseq2_clustering-plot.txt:md5,f5d583266ecc0d0eaddb7a8362405164", - "multiqc_salmon_deseq2_clustering-plot_1.txt:md5,2a1097fe03e12542dd198ed805ba108a", - "multiqc_salmon_deseq2_clustering-plot_2.txt:md5,5f7195951fd89a62b45d16991d0c83d0", - "multiqc_salmon_deseq2_clustering-plot_3.txt:md5,eab5db39f3ee13163329402a87cafd21", - "multiqc_salmon_deseq2_clustering-plot_4.txt:md5,c3287dd65316b9afb54f2c3f6931fa51", "multiqc_samtools_idxstats.txt:md5,1cbc64fc9713831a6f45effc0cfe6a39", "multiqc_star_rsem_deseq2_clustering-plot.txt:md5,62bd581d9ea4cc3fb2dbddeb82238ed2", "multiqc_star_rsem_deseq2_clustering-plot_1.txt:md5,acd14c14552684ef5783a490de0bc704", @@ -939,8 +941,6 @@ "featurecounts_biotype_plot-pct.png:md5,1921c3931d871f8326a6a6c5c8278815", "qualimap_gene_coverage_profile_Counts.png:md5,04a262d5af169d6d771e48555adab37e", "qualimap_gene_coverage_profile_Normalised.png:md5,3bddc4f2a7d462996628e33daf490247", - "rsem_assignment_plot-cnt.png:md5,15fd495eeee0d791d8fe663c9a981b6a", - "rsem_assignment_plot-pct.png:md5,e38d64af2acd404fcdb72a55a6dd1986", "rsem_multimapping_rates.png:md5,e93d35b86e1be681eae9b6ad19e12350", "rseqc_infer_experiment_plot.png:md5,1a3a792e9a6e0c0f93c082594b24e566", "rseqc_read_dups_plot.png:md5,b79c01ce4697ebb7e0ebb4a3da5b44f7", @@ -1143,7 +1143,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-18T14:27:07.132344" + "timestamp": "2024-09-18T15:11:45.123849" }, "Params: --aligner star_rsem - stub": { "content": [ From c26abe5a7d986a3c814696e8b14c35dfbed2fd12 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 18 Sep 2024 16:16:48 +0200 Subject: [PATCH 057/100] better regex --- tests/lib/UTILS.groovy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index 41d7f991b..d9e8a4659 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -133,7 +133,7 @@ class UTILS { /multiqc_rseqc_junction_annotation\.txt/, /multiqc_rseqc_read_distribution\.txt/, /multiqc_salmon\.txt/, - /(star_rsem|multiqc_salmon|multiqc_star_salmon)_deseq2_clustering-plot.*\.(pdf|png|txt)/, + /(star_rsem|multiqc_salmon|multiqc_star_salmon)_deseq2_clustering-plot?.*\.(pdf|png|txt)/, /multiqc_salmon_deseq2_pca-plot.*\.txt/, /multiqc_samtools_flagstat\.txt/, /multiqc_samtools_stats\.txt/, From 79066116644849074897022258859aeabbabff63 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 18 Sep 2024 17:40:58 +0200 Subject: [PATCH 058/100] fix regex --- tests/lib/UTILS.groovy | 47 +++++++++--------------------- tests/remove_ribo_rna.nf.test.snap | 30 +++++++++---------- 2 files changed, 28 insertions(+), 49 deletions(-) diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index d9e8a4659..29528323e 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -133,7 +133,7 @@ class UTILS { /multiqc_rseqc_junction_annotation\.txt/, /multiqc_rseqc_read_distribution\.txt/, /multiqc_salmon\.txt/, - /(star_rsem|multiqc_salmon|multiqc_star_salmon)_deseq2_clustering-plot?.*\.(pdf|png|txt)/, + /(star_rsem|multiqc_salmon|multiqc_star_salmon)_deseq2_clustering-plot?(.*)\.(pdf|png|txt)/, /multiqc_salmon_deseq2_pca-plot.*\.txt/, /multiqc_samtools_flagstat\.txt/, /multiqc_samtools_stats\.txt/, @@ -259,6 +259,7 @@ class UTILS { /samtools_alignment_plot-pct\.svg/, /samtools_alignment_plot\.txt/, /sortmerna-detailed-plot-(cnt|pct)\.(pdf|svg)/, + /sortmerna-detailed-plot\.txt/, /star_alignment_plot-cnt\.pdf/, /star_alignment_plot-cnt\.png/, /star_alignment_plot-cnt\.svg/, @@ -266,14 +267,9 @@ class UTILS { /star_alignment_plot-pct\.png/, /star_alignment_plot-pct\.svg/, /star_alignment_plot\.txt/, - /(star_rsem|star_salmon)_deseq2_(clustering|pca)-plot-\.(pdf|png|svg)/, - /star_salmon_deseq2_pca-plot\.pdf/, - /star_salmon_deseq2_pca-plot\.png/, - /star_salmon_deseq2_pca-plot\.svg/, - /star_summary_table\.pdf/, - /star_summary_table\.png/, - /star_summary_table\.svg/, - /star_summary_table\.txt/, + /(star_rsem|star_salmon)_deseq2_(clustering|pca)-plot?(.*)\.(pdf|png|svg)/, + /star_salmon_deseq2_pca-plot\.(pdf|png|svg)/, + /star_summary_table\.(pdf|png|svg|txt)/, // To exclude from deseq2_qc /RAP1_IAA_30M_REP1\.txt/, @@ -323,8 +319,7 @@ class UTILS { /salmon\.merged\.transcript_tpm\.tsv/, // To exclude bigwig - /.*\.forward\.bigWig/, - /.*\.reverse\.bigWig/, + /.*\.(forward|reverse)\.bigWig/, // To exlude dupradar /.*_duprateExpBoxplot\.pdf/, @@ -335,9 +330,7 @@ class UTILS { /.*\.featureCounts\.txt\.summary/, // To exclude star salmon - /.*\.Log\.final\.out/, - /.*\.Log\.out/, - /.*\.Log\.progress\.out/, + /.*\.Log\.?(final|progress)\.out/, // To exclude Picard Markduplicates metrics /.*\.markdup\.sorted\.MarkDuplicates\.metrics\.txt/, @@ -349,25 +342,12 @@ class UTILS { /rnaseq_qc_results\.txt/, // To exclude rseqc - /.*\.DupRate_plot\.pdf/, - /.*\.DupRate_plot\.r/, - /.*\.inner_distance\.txt/, - /.*\.inner_distance_freq\.txt/, - /.*\.inner_distance_mean\.txt/, - /.*\.inner_distance_plot\.pdf/, - /.*\.inner_distance_plot\.r/, - /.*\.junction\.Interact\.bed/, - /.*\.junction\.bed/, - /.*\.junction\.xls/, - /.*\.junctionSaturation_plot\.pdf/, - /.*\.junctionSaturation_plot\.r/, - /.*\.junction_annotation\.log/, - /.*\.junction_plot\.r/, - /.*\.pos\.DupRate\.xls/, + /.*\.DupRate_plot\.(pdf|r)/, + /.*\.inner_distance.*/, + /.*\.junction.*/, + /.*\.(pos|seq)\.DupRate\.xls/, /.*\.read_distribution\.txt/, - /.*\.seq\.DupRate\.xls/, - /.*\.splice_events\.pdf/, - /.*\.splice_junction\.pdf/, + /.*\.splice_(events|junction)\.pdf/, /.*\.bam_stat\.txt/, // To exclude from samtools stats @@ -393,8 +373,7 @@ class UTILS { /WT_REP2\.log/, // To exclude markdup - /.*\.markdup\.sorted\.bam/, - /.*\.markdup\.sorted\.bam\.bai/, + /.*\.markdup\.sorted\.bam?(\.bai)/, // To exclude trimgalore /.*\.fastq\.gz_trimming_report\.txt/ diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 40aa30e4f..11f34b569 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -205,6 +205,11 @@ "multiqc_rseqc_junction_annotation.txt", "multiqc_rseqc_read_distribution.txt", "multiqc_salmon.txt", + "multiqc_salmon_deseq2_clustering-plot.txt", + "multiqc_salmon_deseq2_clustering-plot_1.txt", + "multiqc_salmon_deseq2_clustering-plot_2.txt", + "multiqc_salmon_deseq2_clustering-plot_3.txt", + "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", "multiqc_samtools_stats.txt", @@ -212,6 +217,11 @@ "multiqc_sortmerna.txt", "multiqc_sources.txt", "multiqc_star.txt", + "multiqc_star_salmon_deseq2_clustering-plot.txt", + "multiqc_star_salmon_deseq2_clustering-plot_1.txt", + "multiqc_star_salmon_deseq2_clustering-plot_2.txt", + "multiqc_star_salmon_deseq2_clustering-plot_3.txt", + "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", "picard_deduplication.txt", "qualimap_genomic_origin.txt", @@ -234,6 +244,7 @@ "samtools-flagstat-dp_Read_counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", + "sortmerna-detailed-plot.txt", "star_alignment_plot.txt", "star_summary_table.txt", "multiqc_report_plots", @@ -309,6 +320,7 @@ "sortmerna-detailed-plot-pct.pdf", "star_alignment_plot-cnt.pdf", "star_alignment_plot-pct.pdf", + "star_salmon_deseq2_clustering-plot.pdf", "star_salmon_deseq2_pca-plot.pdf", "star_summary_table.pdf", "png", @@ -350,6 +362,7 @@ "samtools_alignment_plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", + "star_salmon_deseq2_clustering-plot.png", "star_salmon_deseq2_pca-plot.png", "star_summary_table.png", "svg", @@ -424,6 +437,7 @@ "sortmerna-detailed-plot-pct.svg", "star_alignment_plot-cnt.svg", "star_alignment_plot-pct.svg", + "star_salmon_deseq2_clustering-plot.svg", "star_salmon_deseq2_pca-plot.svg", "star_summary_table.svg", "pipeline_info", @@ -954,17 +968,7 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,54f0eef4ab0ecf6a03505b18752b43cd", - "multiqc_salmon_deseq2_clustering-plot.txt:md5,b84f4797086941a5014d88dc46115832", - "multiqc_salmon_deseq2_clustering-plot_1.txt:md5,7494c2892cc5b058da9e2296f7be5a8c", - "multiqc_salmon_deseq2_clustering-plot_2.txt:md5,4b6e40f595eb28ceaadf43ffe187b752", - "multiqc_salmon_deseq2_clustering-plot_3.txt:md5,d0d2a9e2bf3d4e81fef9b2450e5e29b8", - "multiqc_salmon_deseq2_clustering-plot_4.txt:md5,0ab6a0bc900cb8bae5aa280e2d13397a", "multiqc_samtools_idxstats.txt:md5,413ba06f3d8e4ab0dbde8ef8952c4b32", - "multiqc_star_salmon_deseq2_clustering-plot.txt:md5,99d097781c6761b6894e6bcc7999e1ba", - "multiqc_star_salmon_deseq2_clustering-plot_1.txt:md5,88bcc02233b2df2876678d186df8d32a", - "multiqc_star_salmon_deseq2_clustering-plot_2.txt:md5,8673d08e63e16dc7993f99f15c8377e1", - "multiqc_star_salmon_deseq2_clustering-plot_3.txt:md5,b65a05ab4904d2992d3bf664ad0e82f1", - "multiqc_star_salmon_deseq2_clustering-plot_4.txt:md5,5c77c5fefc953051de1fc1e6d8377cf2", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -975,8 +979,6 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,53addd7b78d8ae224920ec9b97489d72", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,97fc7bde65a7efc5ab3af48ef0400c20", - "sortmerna-detailed-plot.txt:md5,b93dadb4ca77c6af68ef2c00a8626f17", - "star_salmon_deseq2_clustering-plot.pdf:md5,1a1cfea5266d1857da02f0e7c9e062bb", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "dupradar-section-plot.png:md5,62ee84d3b32bdbfb9766fa970680f92c", @@ -1010,8 +1012,6 @@ "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,1a029e5d23f82d537470363a065b644a", "sortmerna-detailed-plot-cnt.png:md5,3875997f21c98e8906cd182d959e0020", "sortmerna-detailed-plot-pct.png:md5,971398875e5cbd50313b6fee7eeb302c", - "star_salmon_deseq2_clustering-plot.png:md5,86ae8d342372b9fe5c8ad3108890606a", - "star_salmon_deseq2_clustering-plot.svg:md5,d414f141d8af259802fb059c8a376ac5", "ambig_info.tsv:md5,25ced9693254994a7878241225baabb6", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -1232,7 +1232,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-18T14:19:29.058683" + "timestamp": "2024-09-18T17:38:19.910241" }, "Params: --remove_ribo_rna - stub": { "content": [ From c5619220323d3cd342087b85316c9ed0fed884f5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 18 Sep 2024 19:28:39 +0200 Subject: [PATCH 059/100] better regex --- tests/lib/UTILS.groovy | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index 29528323e..c1d2d6e11 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -133,7 +133,7 @@ class UTILS { /multiqc_rseqc_junction_annotation\.txt/, /multiqc_rseqc_read_distribution\.txt/, /multiqc_salmon\.txt/, - /(star_rsem|multiqc_salmon|multiqc_star_salmon)_deseq2_clustering-plot?(.*)\.(pdf|png|txt)/, + /(multiqc_)?(salmon|star_salmon|star_rsem)_deseq2_clustering-plot(.*)?\.(pdf|png|txt)/, /multiqc_salmon_deseq2_pca-plot.*\.txt/, /multiqc_samtools_flagstat\.txt/, /multiqc_samtools_stats\.txt/, @@ -267,7 +267,7 @@ class UTILS { /star_alignment_plot-pct\.png/, /star_alignment_plot-pct\.svg/, /star_alignment_plot\.txt/, - /(star_rsem|star_salmon)_deseq2_(clustering|pca)-plot?(.*)\.(pdf|png|svg)/, + /(star_rsem|star_salmon)_deseq2_(clustering|pca)-plot(.*)?\.(pdf|png|svg)/, /star_salmon_deseq2_pca-plot\.(pdf|png|svg)/, /star_summary_table\.(pdf|png|svg|txt)/, @@ -330,7 +330,7 @@ class UTILS { /.*\.featureCounts\.txt\.summary/, // To exclude star salmon - /.*\.Log\.?(final|progress)\.out/, + /.*\.Log\.(final|progress)?\.out/, // To exclude Picard Markduplicates metrics /.*\.markdup\.sorted\.MarkDuplicates\.metrics\.txt/, @@ -373,7 +373,7 @@ class UTILS { /WT_REP2\.log/, // To exclude markdup - /.*\.markdup\.sorted\.bam?(\.bai)/, + /.*\.markdup\.sorted\.bam(\.bai)?/, // To exclude trimgalore /.*\.fastq\.gz_trimming_report\.txt/ From 77e9cc170a063a1de6cb4f44a1fad0514c0e7046 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 19 Sep 2024 09:18:54 +0200 Subject: [PATCH 060/100] update snapshot --- tests/star_rsem.nf.test.snap | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 5cd9614f8..b3bd03300 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -210,6 +210,11 @@ "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", + "multiqc_star_rsem_deseq2_clustering-plot.txt", + "multiqc_star_rsem_deseq2_clustering-plot_1.txt", + "multiqc_star_rsem_deseq2_clustering-plot_2.txt", + "multiqc_star_rsem_deseq2_clustering-plot_3.txt", + "multiqc_star_rsem_deseq2_clustering-plot_4.txt", "picard_deduplication.txt", "qualimap_genomic_origin.txt", "qualimap_rnaseq_genome_results.txt", @@ -902,11 +907,6 @@ "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,27bb37d346e8f0960c882a3676e219e8", "multiqc_samtools_idxstats.txt:md5,1cbc64fc9713831a6f45effc0cfe6a39", - "multiqc_star_rsem_deseq2_clustering-plot.txt:md5,62bd581d9ea4cc3fb2dbddeb82238ed2", - "multiqc_star_rsem_deseq2_clustering-plot_1.txt:md5,acd14c14552684ef5783a490de0bc704", - "multiqc_star_rsem_deseq2_clustering-plot_2.txt:md5,a1e6de655a4e8ec1328afa53fa90322f", - "multiqc_star_rsem_deseq2_clustering-plot_3.txt:md5,826ff3d14aa99c72c5a4280c0ffe21e3", - "multiqc_star_rsem_deseq2_clustering-plot_4.txt:md5,47a6c91d653c82ed64e5be77f919f2c9", "multiqc_star_rsem_deseq2_pca-plot.txt:md5,7a428c83a9dec1f43ecd4fbbea664ece", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1143,7 +1143,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-18T15:11:45.123849" + "timestamp": "2024-09-19T09:17:34.302993" }, "Params: --aligner star_rsem - stub": { "content": [ From d9797884eb8fefd15c7028c553deb3bf9ebfa655 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 19 Sep 2024 09:33:03 +0200 Subject: [PATCH 061/100] code polish --- tests/default.nf.test | 16 ++++++++-------- tests/featurecounts_group_type.nf.test | 16 ++++++++-------- tests/hisat2.nf.test | 16 ++++++++-------- tests/kallisto.nf.test | 16 ++++++++-------- tests/min_mapped_reads.nf.test | 16 ++++++++-------- tests/remove_ribo_rna.nf.test | 16 ++++++++-------- tests/salmon.nf.test | 16 ++++++++-------- tests/skip_qc.nf.test | 16 ++++++++-------- tests/skip_trimming.nf.test | 8 ++++---- tests/star_rsem.nf.test | 16 ++++++++-------- 10 files changed, 76 insertions(+), 76 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 681383290..007f08987 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -12,16 +12,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } @@ -39,16 +39,16 @@ nextflow_pipeline { then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index 8d9990960..8c3af8807 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -13,16 +13,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } @@ -40,16 +40,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index a8365dc14..b3814da42 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -13,16 +13,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } @@ -40,16 +40,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index 7d6397b76..5378ea7f7 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -15,16 +15,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } @@ -44,16 +44,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index 20c75605d..fa0640870 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -13,16 +13,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } @@ -40,16 +40,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index 52bada874..790d9926a 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -13,16 +13,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } @@ -40,16 +40,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index cca7f07aa..254f62e41 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -15,16 +15,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } @@ -44,16 +44,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index dc6f22b31..7dc855cb0 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -13,16 +13,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } @@ -40,16 +40,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index 6b013472b..79d35d7ed 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -13,16 +13,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index f73af622c..7df5ef6eb 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -13,16 +13,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } @@ -40,16 +40,16 @@ nextflow_pipeline { } then { - def path_from_outdir = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) + def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( workflow.trace.tasks().size(), UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - path_from_outdir.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - path_snapshottable + file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + file_snapshottable ).match() } ) } From 742bfa166e8dc62b442fca7dd49db31c583a8517 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 19 Sep 2024 11:23:04 +0200 Subject: [PATCH 062/100] rescue some snaps --- tests/default.nf.test.snap | 6 ++-- tests/featurecounts_group_type.nf.test.snap | 6 ++-- tests/hisat2.nf.test.snap | 6 ++-- tests/kallisto.nf.test.snap | 6 ++-- tests/lib/UTILS.groovy | 38 ++++----------------- tests/min_mapped_reads.nf.test.snap | 6 ++-- tests/remove_ribo_rna.nf.test.snap | 6 ++-- tests/salmon.nf.test.snap | 6 ++-- tests/skip_qc.nf.test.snap | 6 ++-- tests/star_rsem.nf.test.snap | 6 ++-- 10 files changed, 33 insertions(+), 59 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 3869a8acf..235f7b097 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -405,8 +405,6 @@ "star_salmon_deseq2_pca-plot.pdf", "star_summary_table.pdf", "png", - "cutadapt_filtered_reads_plot-cnt.png", - "cutadapt_filtered_reads_plot-pct.png", "fail_strand_check_table.png", "fastqc_adapter_content_plot.png", "fastqc_per_base_n_content_plot-1.png", @@ -1052,6 +1050,8 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", + "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "dupradar-section-plot.png:md5,3ae5e5cb161b7abd878d718bc71b41f6", @@ -1303,6 +1303,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T18:29:56.535818" + "timestamp": "2024-09-19T10:12:58.76862" } } \ No newline at end of file diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index a770cd9ad..c25b46548 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -397,8 +397,6 @@ "star_salmon_deseq2_pca-plot.pdf", "star_summary_table.pdf", "png", - "cutadapt_filtered_reads_plot-cnt.png", - "cutadapt_filtered_reads_plot-pct.png", "fail_strand_check_table.png", "fastqc_adapter_content_plot.png", "fastqc_per_base_n_content_plot-1.png", @@ -1035,6 +1033,8 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", + "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "dupradar-section-plot.png:md5,3ae5e5cb161b7abd878d718bc71b41f6", @@ -1269,6 +1269,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-18T11:13:20.643284" + "timestamp": "2024-09-19T10:21:06.207795" } } \ No newline at end of file diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index c6dcc97bd..9f39f47eb 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -709,8 +709,6 @@ "samtools_alignment_plot-cnt.pdf", "samtools_alignment_plot-pct.pdf", "png", - "cutadapt_filtered_reads_plot-cnt.png", - "cutadapt_filtered_reads_plot-pct.png", "fail_strand_check_table.png", "fastqc_adapter_content_plot.png", "fastqc_per_base_n_content_plot-1.png", @@ -1106,6 +1104,8 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3625f666cc09d0f07990716aeccd869f", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,6c323b383a6506d124506405b9463d93", + "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", + "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "dupradar-section-plot.png:md5,6074ea2315d296094bd10fad3dcc475b", @@ -1175,6 +1175,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-18T15:04:27.247526" + "timestamp": "2024-09-19T10:28:23.826076" } } \ No newline at end of file diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index c6319b7aa..708e58da1 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -156,8 +156,6 @@ "kallisto_alignment-cnt.pdf", "kallisto_alignment-pct.pdf", "png", - "cutadapt_filtered_reads_plot-cnt.png", - "cutadapt_filtered_reads_plot-pct.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot.png", "fastqc_sequence_length_distribution_plot.png", @@ -217,6 +215,8 @@ "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", + "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", + "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890", @@ -233,7 +233,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-18T13:00:14.319235" + "timestamp": "2024-09-19T10:32:38.720378" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index c1d2d6e11..8a6a555e2 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -40,9 +40,8 @@ class UTILS { /.*_fastqc\.html/, // To exclude from the MultiQC reports - /cutadapt_filtered_reads_plot-.*/, - /cutadapt_trimmed_sequences_.*\.pdf/, - /cutadapt_trimmed_sequences_.*\.svg/, + /cutadapt_filtered_reads_plot-(cnt|pct)\.(pdf|svg)/, + /cutadapt_trimmed_sequences_.*\.(pdf|svg)/, /dupradar-section-plot\.pdf/, /dupradar-section-plot\.svg/, /fail_mapped_samples_table.*/, @@ -277,23 +276,11 @@ class UTILS { /RAP1_UNINDUCED_REP2\.txt/, /WT_REP1\.txt/, /WT_REP2\.txt/, - /deseq2\.dds\.RData/, - /deseq2\.pca\.vals\.txt/, - /deseq2\.plots\.pdf/, - /deseq2\.sample\.dists\.txt/, - /deseq2\.size_factors\.RData/, + /deseq2.*/, // To exclude from kallisto /abundance\.tsv/, /kallisto_quant\.log/, - /kallisto\.merged\.gene_counts\.tsv/, - /kallisto\.merged\.gene_counts_length_scaled\.tsv/, - /kallisto\.merged\.gene_counts_scaled\.tsv/, - /kallisto\.merged\.gene_lengths\.tsv/, - /kallisto\.merged\.gene_tpm\.tsv/, - /kallisto\.merged\.transcript_counts\.tsv/, - /kallisto\.merged\.transcript_lengths\.tsv/, - /kallisto\.merged\.transcript_tpm\.tsv/, /run_info\.json/, // To exclude from salmon quant @@ -304,27 +291,14 @@ class UTILS { /quant\.genes\.sf/, /quant\.sf/, - // To exclude from salmon - /salmon\.merged\.gene_counts\.SummarizedExperiment\.rds/, - /salmon\.merged\.gene_counts\.tsv/, - /salmon\.merged\.gene_counts_length_scaled\.SummarizedExperiment\.rds/, - /salmon\.merged\.gene_counts_length_scaled\.tsv/, - /salmon\.merged\.gene_counts_scaled\.SummarizedExperiment\.rds/, - /salmon\.merged\.gene_counts_scaled\.tsv/, - /salmon\.merged\.gene_lengths\.tsv/, - /salmon\.merged\.gene_tpm\.tsv/, - /salmon\.merged\.transcript_counts\.SummarizedExperiment\.rds/, - /salmon\.merged\.transcript_counts\.tsv/, - /salmon\.merged\.transcript_lengths\.tsv/, - /salmon\.merged\.transcript_tpm\.tsv/, + // To exclude from kallisto|salmon aligners + /(kallisto|salmon)\.merged.*/, // To exclude bigwig /.*\.(forward|reverse)\.bigWig/, // To exlude dupradar - /.*_duprateExpBoxplot\.pdf/, - /.*_expressionHist\.pdf/, - /.*_duprateExpDens\.pdf/, + /.*_(duprateExpBoxplot|duprateExpDens|expressionHist)\.pdf/, // To exclude featurecounts /.*\.featureCounts\.txt\.summary/, diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index ceab4f3dd..38c70dccb 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -315,8 +315,6 @@ "star_salmon_deseq2_pca-plot.pdf", "star_summary_table.pdf", "png", - "cutadapt_filtered_reads_plot-cnt.png", - "cutadapt_filtered_reads_plot-pct.png", "fail_mapped_samples_table.png", "fail_strand_check_table.png", "fastqc_adapter_content_plot.png", @@ -855,6 +853,8 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", + "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "dupradar-section-plot.png:md5,eacbc664cc29a7a59a6aa366b4618582", @@ -1046,7 +1046,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-18T13:07:21.624648" + "timestamp": "2024-09-19T10:41:32.333555" }, "Params: --min_mapped_reads 90 - stub": { "content": [ diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 11f34b569..d73fc190a 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -324,8 +324,6 @@ "star_salmon_deseq2_pca-plot.pdf", "star_summary_table.pdf", "png", - "cutadapt_filtered_reads_plot-cnt.png", - "cutadapt_filtered_reads_plot-pct.png", "fail_strand_check_table.png", "fastqc_adapter_content_plot.png", "fastqc_per_base_n_content_plot-1.png", @@ -979,6 +977,8 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,53addd7b78d8ae224920ec9b97489d72", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,97fc7bde65a7efc5ab3af48ef0400c20", + "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", + "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "dupradar-section-plot.png:md5,62ee84d3b32bdbfb9766fa970680f92c", @@ -1232,7 +1232,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-18T17:38:19.910241" + "timestamp": "2024-09-19T10:54:06.730344" }, "Params: --remove_ribo_rna - stub": { "content": [ diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index a79bb4ec9..ecd8d2e93 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -111,8 +111,6 @@ "general_stats_table.pdf", "salmon_plot.pdf", "png", - "cutadapt_filtered_reads_plot-cnt.png", - "cutadapt_filtered_reads_plot-pct.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot.png", "fastqc_sequence_length_distribution_plot.png", @@ -232,6 +230,8 @@ "multiqc_citations.txt:md5,f789abe663d4b4214f0ddeb413a7f150", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", + "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", + "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890", @@ -279,7 +279,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T19:13:06.946699" + "timestamp": "2024-09-19T10:58:01.584391" }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index cfd6fbaea..804c4d71c 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -256,8 +256,6 @@ "star_alignment_plot-pct.pdf", "star_summary_table.pdf", "png", - "cutadapt_filtered_reads_plot-cnt.png", - "cutadapt_filtered_reads_plot-pct.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot.png", "fastqc_sequence_length_distribution_plot.png", @@ -573,6 +571,8 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", + "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890", @@ -677,6 +677,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T19:23:30.52516" + "timestamp": "2024-09-19T11:04:14.333102" } } \ No newline at end of file diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index b3bd03300..ea0b5a1e4 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -313,8 +313,6 @@ "star_rsem_deseq2_clustering-plot.pdf", "star_rsem_deseq2_pca-plot.pdf", "png", - "cutadapt_filtered_reads_plot-cnt.png", - "cutadapt_filtered_reads_plot-pct.png", "fail_strand_check_table.png", "fastqc_adapter_content_plot.png", "fastqc_per_base_n_content_plot-1.png", @@ -918,6 +916,8 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3e67e07b5c978fa363965e8e90356eef", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,a83e44c5a22e014d377c41419175784c", + "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", + "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "dupradar-section-plot.png:md5,f76a34d2eb6f2351729d79efc1434ee8", @@ -1143,7 +1143,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T09:17:34.302993" + "timestamp": "2024-09-19T11:19:40.881884" }, "Params: --aligner star_rsem - stub": { "content": [ From c9e8d0f5c341adb9dee7f68fbc7dc63d89e260d3 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Thu, 19 Sep 2024 12:42:34 +0200 Subject: [PATCH 063/100] Apply suggestions from code review Co-authored-by: Jonathan Manning --- tests/lib/UTILS.groovy | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index 8a6a555e2..09475f052 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -7,14 +7,22 @@ class UTILS { } // Recursively list all files in a directory and its sub-directories, matching or not matching supplied suffixes - public static getAllFilesFromDir(dir, List includeRegexes = null, List excludeRegexes = null) { + public static getAllFilesFromDir(dir, List includeRegexes = null, List excludeRegexes = null, boolean relativePaths = false) { def output = [] - new File(dir).eachFileRecurse() { file -> + def dirFile = new File(dir) + dirFile.eachFileRecurse { file -> boolean matchesInclusion = includeRegexes ? includeRegexes.any { regex -> file.name.toString() ==~ regex } : true boolean matchesExclusion = excludeRegexes ? excludeRegexes.any { regex -> file.name.toString() ==~ regex } : false // Add files to the list if they match the includeRegexes and not the excludeRegexes - if (matchesInclusion && !matchesExclusion) output.add(file) + if (matchesInclusion && !matchesExclusion) { + if (relativePaths) { + def relativePath = dirFile.toURI().relativize(file.toURI()).getPath() + output.add(new File(relativePath)) + } else { + output.add(file) + } + } } return output.sort { it.path } } From 26f3993af5bc3efe071ec1214aa2dfa12766963f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 19 Sep 2024 14:07:29 +0200 Subject: [PATCH 064/100] tiny refactor part I --- tests/default.nf.test | 29 +++++++++++++++------- tests/featurecounts_group_type.nf.test | 28 +++++++++++++++------- tests/hisat2.nf.test | 28 +++++++++++++++------- tests/kallisto.nf.test | 28 +++++++++++++++------- tests/lib/UTILS.groovy | 33 +++++++++----------------- tests/min_mapped_reads.nf.test | 28 +++++++++++++++------- tests/remove_ribo_rna.nf.test | 28 +++++++++++++++------- tests/salmon.nf.test | 28 +++++++++++++++------- tests/skip_qc.nf.test | 28 +++++++++++++++------- tests/skip_trimming.nf.test | 14 +++++++---- tests/star_rsem.nf.test | 28 +++++++++++++++------- 11 files changed, 201 insertions(+), 99 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 007f08987..ede946781 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -12,16 +12,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } @@ -38,17 +44,22 @@ nextflow_pipeline { } then { - - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index 8c3af8807..ffe7c9e38 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -13,16 +13,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } @@ -40,16 +46,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index b3814da42..0cde63dd7 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -13,16 +13,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } @@ -40,16 +46,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index 5378ea7f7..977a03206 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -15,16 +15,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } @@ -44,16 +50,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index 09475f052..ed13fb6a0 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -7,45 +7,34 @@ class UTILS { } // Recursively list all files in a directory and its sub-directories, matching or not matching supplied suffixes - public static getAllFilesFromDir(dir, List includeRegexes = null, List excludeRegexes = null, boolean relativePaths = false) { + public static getAllFilesFromDir(outdir, boolean includeDir = true, List excludeRegexes = null) { def output = [] - def dirFile = new File(dir) - dirFile.eachFileRecurse { file -> - boolean matchesInclusion = includeRegexes ? includeRegexes.any { regex -> file.name.toString() ==~ regex } : true + new File(outdir).eachFileRecurse() { file -> + boolean matchesInclusion = includeDir ? true : file.isFile() boolean matchesExclusion = excludeRegexes ? excludeRegexes.any { regex -> file.name.toString() ==~ regex } : false - // Add files to the list if they match the includeRegexes and not the excludeRegexes - if (matchesInclusion && !matchesExclusion) { - if (relativePaths) { - def relativePath = dirFile.toURI().relativize(file.toURI()).getPath() - output.add(new File(relativePath)) - } else { - output.add(file) - } - } + // Add files (or folders if includeDir is set to true) to the list that don't match excludeRegexes + if (matchesInclusion && !matchesExclusion) output.add(file) } return output.sort { it.path } } // Static (global) exclusion regexes list static List exclusionRegexesForUnstableFileNames = [/.*\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}.*/] - // These are the extension of all files to try to snapshot - static List snapshottablePatterns = [/.*\.(ctab|fasta|gtf|gz|html|json|log|pdf|png|svg|tab|tsv|txt|yml)$/] - // These are the files to exclude when we want to snapshot static List exclusionRegexesForUnstableFileContents = [ - // To exclude files with timestamps in the format YYYY-MM-DD_HH-MM-SS - /.*\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}.*/, - // To exlude the pipeline_software_mqc_versions.yml file that contains the Nextflow version - /nf_core_rnaseq_software_mqc_versions\.yml/, + /nf_core_.*_software_mqc_versions\.yml/, + + // To exlude this folder that somehow is a file on stub tests + /multiqc_plots/, // To exlude bbsplit files /.*\.stats\.txt/, // To exclude FASTQC reports - /.*_raw\.html/, - /.*_fastqc\.html/, + /.*_raw\.(html|zip)/, + /.*_fastqc\.(html|zip)/, // To exclude from the MultiQC reports /cutadapt_filtered_reads_plot-(cnt|pct)\.(pdf|svg)/, diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index fa0640870..9e83cba35 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -13,16 +13,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } @@ -40,16 +46,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index 790d9926a..c415e286e 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -13,16 +13,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } @@ -40,16 +46,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index 254f62e41..622e44594 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -15,16 +15,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } @@ -44,16 +50,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index 7dc855cb0..079918440 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -13,16 +13,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } @@ -40,16 +46,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index 79d35d7ed..88d644aab 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -13,16 +13,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 7df5ef6eb..ee7636338 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -13,16 +13,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } @@ -40,16 +46,22 @@ nextflow_pipeline { } then { - def file_complement = UTILS.getAllFilesFromDir(params.outdir, null, UTILS.exclusionRegexesForUnstableFileNames) - def file_snapshottable = UTILS.getAllFilesFromDir(params.outdir, UTILS.snapshottablePatterns, UTILS.exclusionRegexesForUnstableFileContents) + // path_name_stable: All files + folders in ${params.outdir}/ with a stable name + def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // path_snapshottable: All files in ${params.outdir}/ with stable content + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( + // Number of tasks workflow.trace.tasks().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file_complement.collect{ file -> file_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, - file_snapshottable + // All stable path from which we remove files with stable contents + path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All files with stable contents + path_snapshottable ).match() } ) } From e44a03c78984d5607c87655892dbbd2270336989 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 19 Sep 2024 14:27:34 +0200 Subject: [PATCH 065/100] tiny refactor part II - IT IS GROOVY WE CAN SUBSTRACT :facepalm: --- tests/default.nf.test | 10 ++++------ tests/featurecounts_group_type.nf.test | 10 ++++------ tests/hisat2.nf.test | 10 ++++------ tests/kallisto.nf.test | 10 ++++------ tests/min_mapped_reads.nf.test | 10 ++++------ tests/remove_ribo_rna.nf.test | 10 ++++------ tests/salmon.nf.test | 10 ++++------ tests/skip_qc.nf.test | 10 ++++------ tests/skip_trimming.nf.test | 5 ++--- tests/star_rsem.nf.test | 10 ++++------ 10 files changed, 38 insertions(+), 57 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index ede946781..2c40f317f 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -16,7 +16,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -24,8 +23,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -48,7 +47,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -56,8 +54,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index ffe7c9e38..7496f4aee 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -17,7 +17,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -25,8 +24,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -50,7 +49,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -58,8 +56,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 0cde63dd7..2d3cb8e0b 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -17,7 +17,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -25,8 +24,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -50,7 +49,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -58,8 +56,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index 977a03206..001a467df 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -19,7 +19,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -27,8 +26,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -54,7 +53,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -62,8 +60,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index 9e83cba35..f2b857136 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -17,7 +17,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -25,8 +24,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -50,7 +49,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -58,8 +56,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index c415e286e..df264b9eb 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -17,7 +17,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -25,8 +24,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -50,7 +49,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -58,8 +56,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index 622e44594..c561d7487 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -19,7 +19,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -27,8 +26,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -54,7 +53,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -62,8 +60,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index 079918440..9d2d6291d 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -17,7 +17,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -25,8 +24,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -50,7 +49,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -58,8 +56,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index 88d644aab..8df873f4a 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -17,7 +17,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -25,8 +24,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index ee7636338..664d07cc5 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -17,7 +17,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -25,8 +24,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -50,7 +49,6 @@ nextflow_pipeline { def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) - assertAll( { assert workflow.success}, { assert snapshot( @@ -58,8 +56,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path from which we remove files with stable contents - path_name_stable.collect{ file -> path_snapshottable.contains(file) ? null : file.getName()}.findAll{ it }, + // All stable path name from which we remove files with stable contents + (path_name_stable - path_snapshottable).collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } From ed2cf1f6f4d722cf6b9d7f2e6006690646c15cc3 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 19 Sep 2024 14:43:26 +0200 Subject: [PATCH 066/100] update regexes --- tests/lib/UTILS.groovy | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index ed13fb6a0..2e0139403 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -23,13 +23,18 @@ class UTILS { // These are the files to exclude when we want to snapshot static List exclusionRegexesForUnstableFileContents = [ - // To exlude the pipeline_software_mqc_versions.yml file that contains the Nextflow version + // To exclude the pipeline_software_mqc_versions.yml file that contains the Nextflow version /nf_core_.*_software_mqc_versions\.yml/, - // To exlude this folder that somehow is a file on stub tests + // To exclude this folder that somehow is a file on stub tests /multiqc_plots/, - // To exlude bbsplit files + // To exclude from qualimap css folders + /.*\.css/, + /.*\.gif/, + /.*\.js/, + + // To exclude bbsplit files /.*\.stats\.txt/, // To exclude FASTQC reports @@ -276,7 +281,7 @@ class UTILS { /deseq2.*/, // To exclude from kallisto - /abundance\.tsv/, + /abundance\.(h5|tsv)/, /kallisto_quant\.log/, /run_info\.json/, @@ -294,14 +299,14 @@ class UTILS { // To exclude bigwig /.*\.(forward|reverse)\.bigWig/, - // To exlude dupradar + // To exclude dupradar /.*_(duprateExpBoxplot|duprateExpDens|expressionHist)\.pdf/, // To exclude featurecounts /.*\.featureCounts\.txt\.summary/, // To exclude star salmon - /.*\.Log\.(final|progress)?\.out/, + /.*\.Log\.?(final|progress)?\.out/, // To exclude Picard Markduplicates metrics /.*\.markdup\.sorted\.MarkDuplicates\.metrics\.txt/, From 92349227306ef8fd7c8ea76d0aaff934acae1fd4 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 19 Sep 2024 15:07:50 +0200 Subject: [PATCH 067/100] move pipeline regexes in UTILS_PIPELINE --- tests/default.nf.test | 4 +- tests/featurecounts_group_type.nf.test | 4 +- tests/hisat2.nf.test | 4 +- tests/kallisto.nf.test | 4 +- tests/lib/UTILS.groovy | 335 ------------------------- tests/lib/UTILS_PIPELINE.groovy | 326 ++++++++++++++++++++++++ tests/min_mapped_reads.nf.test | 4 +- tests/remove_ribo_rna.nf.test | 4 +- tests/salmon.nf.test | 4 +- tests/skip_qc.nf.test | 4 +- tests/skip_trimming.nf.test | 2 +- tests/star_rsem.nf.test | 4 +- 12 files changed, 345 insertions(+), 354 deletions(-) create mode 100644 tests/lib/UTILS_PIPELINE.groovy diff --git a/tests/default.nf.test b/tests/default.nf.test index 2c40f317f..48ebd1d27 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -15,7 +15,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -46,7 +46,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index 7496f4aee..3cfa81189 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -16,7 +16,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -48,7 +48,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 2d3cb8e0b..76d2c8ea7 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -16,7 +16,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -48,7 +48,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index 001a467df..a232dc9c7 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -18,7 +18,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -52,7 +52,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy index 2e0139403..48500bd3f 100644 --- a/tests/lib/UTILS.groovy +++ b/tests/lib/UTILS.groovy @@ -20,339 +20,4 @@ class UTILS { } // Static (global) exclusion regexes list static List exclusionRegexesForUnstableFileNames = [/.*\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}.*/] - - // These are the files to exclude when we want to snapshot - static List exclusionRegexesForUnstableFileContents = [ - // To exclude the pipeline_software_mqc_versions.yml file that contains the Nextflow version - /nf_core_.*_software_mqc_versions\.yml/, - - // To exclude this folder that somehow is a file on stub tests - /multiqc_plots/, - - // To exclude from qualimap css folders - /.*\.css/, - /.*\.gif/, - /.*\.js/, - - // To exclude bbsplit files - /.*\.stats\.txt/, - - // To exclude FASTQC reports - /.*_raw\.(html|zip)/, - /.*_fastqc\.(html|zip)/, - - // To exclude from the MultiQC reports - /cutadapt_filtered_reads_plot-(cnt|pct)\.(pdf|svg)/, - /cutadapt_trimmed_sequences_.*\.(pdf|svg)/, - /dupradar-section-plot\.pdf/, - /dupradar-section-plot\.svg/, - /fail_mapped_samples_table.*/, - /fail_strand_check_table.*/, - /fastqc-status-check-.*\.pdf/, - /fastqc-status-check-.*\.svg/, - /fastqc_adapter_content_plot\.pdf/, - /fastqc_adapter_content_plot\.png/, - /fastqc_adapter_content_plot\.svg/, - /fastqc_overrepresented_sequences_plot-1\.pdf/, - /fastqc_overrepresented_sequences_plot-1\.svg/, - /fastqc_overrepresented_sequences_plot\.pdf/, - /fastqc_overrepresented_sequences_plot\.svg/, - /fastqc_per_base_n_content_plot-1\.pdf/, - /fastqc_per_base_n_content_plot-1\.png/, - /fastqc_per_base_n_content_plot-1\.svg/, - /fastqc_per_base_n_content_plot\.pdf/, - /fastqc_per_base_n_content_plot\.png/, - /fastqc_per_base_n_content_plot\.svg/, - /fastqc_per_base_sequence_quality_plot-1\.pdf/, - /fastqc_per_base_sequence_quality_plot-1\.png/, - /fastqc_per_base_sequence_quality_plot-1\.svg/, - /fastqc_per_base_sequence_quality_plot\.pdf/, - /fastqc_per_base_sequence_quality_plot\.png/, - /fastqc_per_base_sequence_quality_plot\.svg/, - /fastqc_per_sequence_gc_content_plot-1_Counts\.pdf/, - /fastqc_per_sequence_gc_content_plot-1_Counts\.svg/, - /fastqc_per_sequence_gc_content_plot-1_Percentages\.pdf/, - /fastqc_per_sequence_gc_content_plot-1_Percentages\.svg/, - /fastqc_per_sequence_gc_content_plot_Counts\.pdf/, - /fastqc_per_sequence_gc_content_plot_Counts\.svg/, - /fastqc_per_sequence_gc_content_plot_Percentages\.pdf/, - /fastqc_per_sequence_gc_content_plot_Percentages\.svg/, - /fastqc_per_sequence_quality_scores_plot-1\.pdf/, - /fastqc_per_sequence_quality_scores_plot-1\.svg/, - /fastqc_per_sequence_quality_scores_plot\.pdf/, - /fastqc_per_sequence_quality_scores_plot\.svg/, - /fastqc_sequence_counts_plot-1-cnt\.pdf/, - /fastqc_sequence_counts_plot-1-cnt\.svg/, - /fastqc_sequence_counts_plot-1-pct\.pdf/, - /fastqc_sequence_counts_plot-1-pct\.svg/, - /fastqc_sequence_counts_plot-cnt\.pdf/, - /fastqc_sequence_counts_plot-cnt\.svg/, - /fastqc_sequence_counts_plot-pct\.pdf/, - /fastqc_sequence_counts_plot-pct\.svg/, - /fastqc_sequence_duplication_levels_plot-1\.pdf/, - /fastqc_sequence_duplication_levels_plot-1\.svg/, - /fastqc_sequence_duplication_levels_plot\.pdf/, - /fastqc_sequence_duplication_levels_plot\.svg/, - /fastqc_sequence_length_distribution_plot\.pdf/, - /fastqc_sequence_length_distribution_plot\.png/, - /fastqc_sequence_length_distribution_plot\.svg/, - /fastqc_top_overrepresented_sequences_table-1\.pdf/, - /fastqc_top_overrepresented_sequences_table-1\.png/, - /fastqc_top_overrepresented_sequences_table-1\.svg/, - /fastqc_top_overrepresented_sequences_table-1\.txt/, - /fastqc_top_overrepresented_sequences_table\.pdf/, - /fastqc_top_overrepresented_sequences_table\.png/, - /fastqc_top_overrepresented_sequences_table\.svg/, - /fastqc_top_overrepresented_sequences_table\.txt/, - /featurecounts_biotype_plot-cnt\.pdf/, - /featurecounts_biotype_plot-cnt\.svg/, - /featurecounts_biotype_plot-pct\.pdf/, - /featurecounts_biotype_plot-pct\.svg/, - /general_stats_table\.pdf/, - /general_stats_table\.png/, - /general_stats_table\.svg/, - /hisat2_(pe|se)_plot-(cnt|pct)\.(pdf|png|svg)/, - /hisat2_pe_plot\.txt/, - /hisat2_se_plot.*\.(png|svg)/, - /junction_saturation_known\.txt/, - /junction_saturation_novel\.txt/, - /kallisto_alignment.*.pdf/, - /kallisto_alignment.*.png/, - /kallisto_alignment.*.svg/, - /kallisto_alignment\.txt/, - /multiqc_data\.json/, - /multiqc_dupradar-section-plot\.txt/, - /multiqc_fail_strand_check_table\.txt/, - /multiqc_general_stats\.txt/, - /multiqc_hisat2\.txt/, - /multiqc_kallisto\.txt/, - /multiqc_picard_dups\.txt/, - /multiqc_report\.html/, - /multiqc_rsem\.txt/, - /multiqc_rseqc_bam_stat\.txt/, - /multiqc_rseqc_infer_experiment\.txt/, - /multiqc_rseqc_junction_annotation\.txt/, - /multiqc_rseqc_read_distribution\.txt/, - /multiqc_salmon\.txt/, - /(multiqc_)?(salmon|star_salmon|star_rsem)_deseq2_clustering-plot(.*)?\.(pdf|png|txt)/, - /multiqc_salmon_deseq2_pca-plot.*\.txt/, - /multiqc_samtools_flagstat\.txt/, - /multiqc_samtools_stats\.txt/, - /multiqc_software_versions\.txt/, - /multiqc_sortmerna\.txt/, - /multiqc_sources\.txt/, - /multiqc_star\.txt/, - /multiqc_star_salmon_deseq2_pca-plot\.txt/, - /picard_deduplication-cnt\.pdf/, - /picard_deduplication-cnt\.png/, - /picard_deduplication-cnt\.svg/, - /picard_deduplication-pct\.pdf/, - /picard_deduplication-pct\.png/, - /picard_deduplication-pct\.svg/, - /picard_deduplication\.txt/, - /qualimap_gene_coverage_profile_Counts\.pdf/, - /qualimap_gene_coverage_profile_Counts\.svg/, - /qualimap_gene_coverage_profile_Normalised\.pdf/, - /qualimap_gene_coverage_profile_Normalised\.svg/, - /qualimap_genomic_origin-cnt\.pdf/, - /qualimap_genomic_origin-cnt\.png/, - /qualimap_genomic_origin-cnt\.svg/, - /qualimap_genomic_origin-pct\.pdf/, - /qualimap_genomic_origin-pct\.png/, - /qualimap_genomic_origin-pct\.svg/, - /qualimap_genomic_origin\.txt/, - /qualimap_rnaseq_genome_results\.txt/, - /rsem_assignment_plot\.txt/, - /rsem_assignment_plot-(cnt|pct)\.(pdf|png|svg)/, - /rsem_multimapping_rates\.(pdf|svg|txt)/, - /rseqc_bam_stat\.pdf/, - /rseqc_bam_stat\.png/, - /rseqc_bam_stat\.svg/, - /rseqc_bam_stat\.txt/, - /rseqc_infer_experiment_plot\.pdf/, - /rseqc_infer_experiment_plot\.svg/, - /rseqc_inner_distance\.txt/, - /rseqc_inner_distance_plot_Counts\.pdf/, - /rseqc_inner_distance_plot_Counts\.png/, - /rseqc_inner_distance_plot_Counts\.svg/, - /rseqc_inner_distance_plot_Counts\.txt/, - /rseqc_inner_distance_plot_Percentages\.pdf/, - /rseqc_inner_distance_plot_Percentages\.png/, - /rseqc_inner_distance_plot_Percentages\.svg/, - /rseqc_inner_distance_plot_Percentages\.txt/, - /rseqc_junction_annotation_junctions_plot_Events-cnt\.pdf/, - /rseqc_junction_annotation_junctions_plot_Events-cnt\.png/, - /rseqc_junction_annotation_junctions_plot_Events-cnt\.svg/, - /rseqc_junction_annotation_junctions_plot_Events-pct\.pdf/, - /rseqc_junction_annotation_junctions_plot_Events-pct\.png/, - /rseqc_junction_annotation_junctions_plot_Events-pct\.svg/, - /rseqc_junction_annotation_junctions_plot_Events\.txt/, - /rseqc_junction_annotation_junctions_plot_Junctions-cnt\.pdf/, - /rseqc_junction_annotation_junctions_plot_Junctions-cnt\.png/, - /rseqc_junction_annotation_junctions_plot_Junctions-cnt\.svg/, - /rseqc_junction_annotation_junctions_plot_Junctions-pct\.pdf/, - /rseqc_junction_annotation_junctions_plot_Junctions-pct\.png/, - /rseqc_junction_annotation_junctions_plot_Junctions-pct\.svg/, - /rseqc_junction_annotation_junctions_plot_Junctions\.txt/, - /rseqc_junction_saturation_all\.txt/, - /rseqc_junction_saturation_plot_All_Junctions\.pdf/, - /rseqc_junction_saturation_plot_All_Junctions\.png/, - /rseqc_junction_saturation_plot_All_Junctions\.svg/, - /rseqc_junction_saturation_plot_All_Junctions\.txt/, - /rseqc_junction_saturation_plot_Known_Junctions\.pdf/, - /rseqc_junction_saturation_plot_Known_Junctions\.png/, - /rseqc_junction_saturation_plot_Known_Junctions\.svg/, - /rseqc_junction_saturation_plot_Known_Junctions\.txt/, - /rseqc_junction_saturation_plot_Novel_Junctions\.pdf/, - /rseqc_junction_saturation_plot_Novel_Junctions\.png/, - /rseqc_junction_saturation_plot_Novel_Junctions\.svg/, - /rseqc_junction_saturation_plot_Novel_Junctions\.txt/, - /rseqc_read_distribution_plot-cnt\.pdf/, - /rseqc_read_distribution_plot-cnt\.png/, - /rseqc_read_distribution_plot-cnt\.svg/, - /rseqc_read_distribution_plot-pct\.pdf/, - /rseqc_read_distribution_plot-pct\.png/, - /rseqc_read_distribution_plot-pct\.svg/, - /rseqc_read_distribution_plot\.txt/, - /rseqc_read_dups\.txt/, - /rseqc_read_dups_plot\.pdf/, - /rseqc_read_dups_plot\.svg/, - /rseqc_read_dups_plot\.txt/, - /(salmon|star_rsem)_deseq2_(clustering|pca)-plot\.pdf/, - /(salmon|star_rsem)_deseq2_(clustering|pca)-plot\.png/, - /(salmon|star_rsem)_deseq2_(clustering|pca)-plot\.svg/, - /(salmon|star_rsem)_deseq2_(pca|pca)-plot\.pdf/, - /(salmon|star_rsem)_deseq2_(pca|pca)-plot\.png/, - /(salmon|star_rsem)_deseq2_(pca|pca)-plot\.svg/, - /salmon_plot\.pdf/, - /salmon_plot\.png/, - /salmon_plot\.svg/, - /salmon_plot\.txt/, - /samtools-flagstat-dp_Percentage_of_total\.pdf/, - /samtools-flagstat-dp_Percentage_of_total\.png/, - /samtools-flagstat-dp_Percentage_of_total\.svg/, - /samtools-flagstat-dp_Percentage_of_total\.txt/, - /samtools-flagstat-dp_Read_counts\.pdf/, - /samtools-flagstat-dp_Read_counts\.png/, - /samtools-flagstat-dp_Read_counts\.svg/, - /samtools-flagstat-dp_Read_counts\.txt/, - /samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt\.pdf/, - /samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt\.svg/, - /samtools-idxstats-mapped-reads-plot_Normalised_Counts-log\.pdf/, - /samtools-idxstats-mapped-reads-plot_Normalised_Counts-log\.svg/, - /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt\.pdf/, - /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt\.svg/, - /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log\.pdf/, - /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log\.svg/, - /samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt\.pdf/, - /samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt\.svg/, - /samtools-idxstats-mapped-reads-plot_Raw_Counts-log\.pdf/, - /samtools-idxstats-mapped-reads-plot_Raw_Counts-log\.svg/, - /samtools-stats-dp\.pdf/, - /samtools-stats-dp\.png/, - /samtools-stats-dp\.svg/, - /samtools-stats-dp\.txt/, - /samtools_alignment_plot-cnt\.pdf/, - /samtools_alignment_plot-cnt\.png/, - /samtools_alignment_plot-cnt\.svg/, - /samtools_alignment_plot-pct\.pdf/, - /samtools_alignment_plot-pct\.png/, - /samtools_alignment_plot-pct\.svg/, - /samtools_alignment_plot\.txt/, - /sortmerna-detailed-plot-(cnt|pct)\.(pdf|svg)/, - /sortmerna-detailed-plot\.txt/, - /star_alignment_plot-cnt\.pdf/, - /star_alignment_plot-cnt\.png/, - /star_alignment_plot-cnt\.svg/, - /star_alignment_plot-pct\.pdf/, - /star_alignment_plot-pct\.png/, - /star_alignment_plot-pct\.svg/, - /star_alignment_plot\.txt/, - /(star_rsem|star_salmon)_deseq2_(clustering|pca)-plot(.*)?\.(pdf|png|svg)/, - /star_salmon_deseq2_pca-plot\.(pdf|png|svg)/, - /star_summary_table\.(pdf|png|svg|txt)/, - - // To exclude from deseq2_qc - /RAP1_IAA_30M_REP1\.txt/, - /RAP1_UNINDUCED_REP1\.txt/, - /RAP1_UNINDUCED_REP2\.txt/, - /WT_REP1\.txt/, - /WT_REP2\.txt/, - /deseq2.*/, - - // To exclude from kallisto - /abundance\.(h5|tsv)/, - /kallisto_quant\.log/, - /run_info\.json/, - - // To exclude from salmon quant - /fld\.gz/, - /meta_info\.json/, - /flenDist\.txt/, - /salmon_quant\.log/, - /quant\.genes\.sf/, - /quant\.sf/, - - // To exclude from kallisto|salmon aligners - /(kallisto|salmon)\.merged.*/, - - // To exclude bigwig - /.*\.(forward|reverse)\.bigWig/, - - // To exclude dupradar - /.*_(duprateExpBoxplot|duprateExpDens|expressionHist)\.pdf/, - - // To exclude featurecounts - /.*\.featureCounts\.txt\.summary/, - - // To exclude star salmon - /.*\.Log\.?(final|progress)?\.out/, - - // To exclude Picard Markduplicates metrics - /.*\.markdup\.sorted\.MarkDuplicates\.metrics\.txt/, - - // To exclude Qualimap files - /Junction\sAnalysis\.png/, - /Reads\sGenomic\sOrigin\.png/, - /qualimapReport\.html/, - /rnaseq_qc_results\.txt/, - - // To exclude rseqc - /.*\.DupRate_plot\.(pdf|r)/, - /.*\.inner_distance.*/, - /.*\.junction.*/, - /.*\.(pos|seq)\.DupRate\.xls/, - /.*\.read_distribution\.txt/, - /.*\.splice_(events|junction)\.pdf/, - /.*\.bam_stat\.txt/, - - // To exclude from samtools stats - /.*\.sorted\.bam\.(flagstat|idxstats|stats)/, - - // To exclude from hisat2 - /.*hisat2\.summary/, - - // To exclude from stringtie - /t_data\.ctab/, - /.*\.coverage\.gtf/, - /.*\.gene\.abundance\.txt/, - /.*\.transcripts\.gtf/, - - // To exclude from sortmerna - /.*\.sortmerna\.log/, - - // To exclude log from star rsem - /RAP1_IAA_30M_REP1\.log/, - /RAP1_UNINDUCED_REP1\.log/, - /RAP1_UNINDUCED_REP2\.log/, - /WT_REP1\.log/, - /WT_REP2\.log/, - - // To exclude markdup - /.*\.markdup\.sorted\.bam(\.bai)?/, - - // To exclude trimgalore - /.*\.fastq\.gz_trimming_report\.txt/ - ] - } diff --git a/tests/lib/UTILS_PIPELINE.groovy b/tests/lib/UTILS_PIPELINE.groovy new file mode 100644 index 000000000..f0074a6cc --- /dev/null +++ b/tests/lib/UTILS_PIPELINE.groovy @@ -0,0 +1,326 @@ +class UTILS_PIPELINE { + // These are the files to exclude when we want to snapshot + static List exclusionRegexesForUnstableFileContents = [ + // To exclude the pipeline_software_mqc_versions.yml file that contains the Nextflow version + /nf_core_.*_software_mqc_versions\.yml/, + + // To exclude this folder that somehow is a file on stub tests + /multiqc_plots/, + + // To exclude from qualimap css folders + /.*\.(css|gif|js)/, + + // To exclude bbsplit files + /.*\.stats\.txt/, + + // To exclude FASTQC reports + /.*_raw\.(html|zip)/, + /.*_fastqc\.(html|zip)/, + + // To exclude from the MultiQC reports + /cutadapt_filtered_reads_plot-(cnt|pct)\.(pdf|svg)/, + /cutadapt_trimmed_sequences_.*\.(pdf|svg)/, + /dupradar-section-plot\.(pdf|svg)/, + /fail_mapped_samples_table.*/, + /fail_strand_check_table.*/, + /fastqc-status-check-.*\.(pdf|svg)/, + /fastqc_adapter_content_plot\.(pdf|png|svg)/, + /fastqc_overrepresented_sequences_plot(.*)?\.(pdf|svg)/, + /fastqc_per_base_n_content_plot-1\.pdf/, + /fastqc_per_base_n_content_plot-1\.png/, + /fastqc_per_base_n_content_plot-1\.svg/, + /fastqc_per_base_n_content_plot\.pdf/, + /fastqc_per_base_n_content_plot\.png/, + /fastqc_per_base_n_content_plot\.svg/, + /fastqc_per_base_sequence_quality_plot-1\.pdf/, + /fastqc_per_base_sequence_quality_plot-1\.png/, + /fastqc_per_base_sequence_quality_plot-1\.svg/, + /fastqc_per_base_sequence_quality_plot\.pdf/, + /fastqc_per_base_sequence_quality_plot\.png/, + /fastqc_per_base_sequence_quality_plot\.svg/, + /fastqc_per_sequence_gc_content_plot-1_Counts\.pdf/, + /fastqc_per_sequence_gc_content_plot-1_Counts\.svg/, + /fastqc_per_sequence_gc_content_plot-1_Percentages\.pdf/, + /fastqc_per_sequence_gc_content_plot-1_Percentages\.svg/, + /fastqc_per_sequence_gc_content_plot_Counts\.pdf/, + /fastqc_per_sequence_gc_content_plot_Counts\.svg/, + /fastqc_per_sequence_gc_content_plot_Percentages\.pdf/, + /fastqc_per_sequence_gc_content_plot_Percentages\.svg/, + /fastqc_per_sequence_quality_scores_plot-1\.pdf/, + /fastqc_per_sequence_quality_scores_plot-1\.svg/, + /fastqc_per_sequence_quality_scores_plot\.pdf/, + /fastqc_per_sequence_quality_scores_plot\.svg/, + /fastqc_sequence_counts_plot-1-cnt\.pdf/, + /fastqc_sequence_counts_plot-1-cnt\.svg/, + /fastqc_sequence_counts_plot-1-pct\.pdf/, + /fastqc_sequence_counts_plot-1-pct\.svg/, + /fastqc_sequence_counts_plot-cnt\.pdf/, + /fastqc_sequence_counts_plot-cnt\.svg/, + /fastqc_sequence_counts_plot-pct\.pdf/, + /fastqc_sequence_counts_plot-pct\.svg/, + /fastqc_sequence_duplication_levels_plot-1\.pdf/, + /fastqc_sequence_duplication_levels_plot-1\.svg/, + /fastqc_sequence_duplication_levels_plot\.pdf/, + /fastqc_sequence_duplication_levels_plot\.svg/, + /fastqc_sequence_length_distribution_plot\.pdf/, + /fastqc_sequence_length_distribution_plot\.png/, + /fastqc_sequence_length_distribution_plot\.svg/, + /fastqc_top_overrepresented_sequences_table-1\.pdf/, + /fastqc_top_overrepresented_sequences_table-1\.png/, + /fastqc_top_overrepresented_sequences_table-1\.svg/, + /fastqc_top_overrepresented_sequences_table-1\.txt/, + /fastqc_top_overrepresented_sequences_table\.pdf/, + /fastqc_top_overrepresented_sequences_table\.png/, + /fastqc_top_overrepresented_sequences_table\.svg/, + /fastqc_top_overrepresented_sequences_table\.txt/, + /featurecounts_biotype_plot-cnt\.pdf/, + /featurecounts_biotype_plot-cnt\.svg/, + /featurecounts_biotype_plot-pct\.pdf/, + /featurecounts_biotype_plot-pct\.svg/, + /general_stats_table\.pdf/, + /general_stats_table\.png/, + /general_stats_table\.svg/, + /hisat2_(pe|se)_plot-(cnt|pct)\.(pdf|png|svg)/, + /hisat2_pe_plot\.txt/, + /hisat2_se_plot.*\.(png|svg)/, + /junction_saturation_known\.txt/, + /junction_saturation_novel\.txt/, + /kallisto_alignment.*.pdf/, + /kallisto_alignment.*.png/, + /kallisto_alignment.*.svg/, + /kallisto_alignment\.txt/, + /multiqc_data\.json/, + /multiqc_dupradar-section-plot\.txt/, + /multiqc_fail_strand_check_table\.txt/, + /multiqc_general_stats\.txt/, + /multiqc_hisat2\.txt/, + /multiqc_kallisto\.txt/, + /multiqc_picard_dups\.txt/, + /multiqc_report\.html/, + /multiqc_rsem\.txt/, + /multiqc_rseqc_bam_stat\.txt/, + /multiqc_rseqc_infer_experiment\.txt/, + /multiqc_rseqc_junction_annotation\.txt/, + /multiqc_rseqc_read_distribution\.txt/, + /multiqc_salmon\.txt/, + /(multiqc_)?(salmon|star_salmon|star_rsem)_deseq2_clustering-plot(.*)?\.(pdf|png|txt)/, + /multiqc_salmon_deseq2_pca-plot.*\.txt/, + /multiqc_samtools_flagstat\.txt/, + /multiqc_samtools_stats\.txt/, + /multiqc_software_versions\.txt/, + /multiqc_sortmerna\.txt/, + /multiqc_sources\.txt/, + /multiqc_star\.txt/, + /multiqc_star_salmon_deseq2_pca-plot\.txt/, + /picard_deduplication-cnt\.pdf/, + /picard_deduplication-cnt\.png/, + /picard_deduplication-cnt\.svg/, + /picard_deduplication-pct\.pdf/, + /picard_deduplication-pct\.png/, + /picard_deduplication-pct\.svg/, + /picard_deduplication\.txt/, + /qualimap_gene_coverage_profile_Counts\.pdf/, + /qualimap_gene_coverage_profile_Counts\.svg/, + /qualimap_gene_coverage_profile_Normalised\.pdf/, + /qualimap_gene_coverage_profile_Normalised\.svg/, + /qualimap_genomic_origin-cnt\.pdf/, + /qualimap_genomic_origin-cnt\.png/, + /qualimap_genomic_origin-cnt\.svg/, + /qualimap_genomic_origin-pct\.pdf/, + /qualimap_genomic_origin-pct\.png/, + /qualimap_genomic_origin-pct\.svg/, + /qualimap_genomic_origin\.txt/, + /qualimap_rnaseq_genome_results\.txt/, + /rsem_assignment_plot\.txt/, + /rsem_assignment_plot-(cnt|pct)\.(pdf|png|svg)/, + /rsem_multimapping_rates\.(pdf|svg|txt)/, + /rseqc_bam_stat\.pdf/, + /rseqc_bam_stat\.png/, + /rseqc_bam_stat\.svg/, + /rseqc_bam_stat\.txt/, + /rseqc_infer_experiment_plot\.pdf/, + /rseqc_infer_experiment_plot\.svg/, + /rseqc_inner_distance\.txt/, + /rseqc_inner_distance_plot_Counts\.pdf/, + /rseqc_inner_distance_plot_Counts\.png/, + /rseqc_inner_distance_plot_Counts\.svg/, + /rseqc_inner_distance_plot_Counts\.txt/, + /rseqc_inner_distance_plot_Percentages\.pdf/, + /rseqc_inner_distance_plot_Percentages\.png/, + /rseqc_inner_distance_plot_Percentages\.svg/, + /rseqc_inner_distance_plot_Percentages\.txt/, + /rseqc_junction_annotation_junctions_plot_Events-cnt\.pdf/, + /rseqc_junction_annotation_junctions_plot_Events-cnt\.png/, + /rseqc_junction_annotation_junctions_plot_Events-cnt\.svg/, + /rseqc_junction_annotation_junctions_plot_Events-pct\.pdf/, + /rseqc_junction_annotation_junctions_plot_Events-pct\.png/, + /rseqc_junction_annotation_junctions_plot_Events-pct\.svg/, + /rseqc_junction_annotation_junctions_plot_Events\.txt/, + /rseqc_junction_annotation_junctions_plot_Junctions-cnt\.pdf/, + /rseqc_junction_annotation_junctions_plot_Junctions-cnt\.png/, + /rseqc_junction_annotation_junctions_plot_Junctions-cnt\.svg/, + /rseqc_junction_annotation_junctions_plot_Junctions-pct\.pdf/, + /rseqc_junction_annotation_junctions_plot_Junctions-pct\.png/, + /rseqc_junction_annotation_junctions_plot_Junctions-pct\.svg/, + /rseqc_junction_annotation_junctions_plot_Junctions\.txt/, + /rseqc_junction_saturation_all\.txt/, + /rseqc_junction_saturation_plot_All_Junctions\.pdf/, + /rseqc_junction_saturation_plot_All_Junctions\.png/, + /rseqc_junction_saturation_plot_All_Junctions\.svg/, + /rseqc_junction_saturation_plot_All_Junctions\.txt/, + /rseqc_junction_saturation_plot_Known_Junctions\.pdf/, + /rseqc_junction_saturation_plot_Known_Junctions\.png/, + /rseqc_junction_saturation_plot_Known_Junctions\.svg/, + /rseqc_junction_saturation_plot_Known_Junctions\.txt/, + /rseqc_junction_saturation_plot_Novel_Junctions\.pdf/, + /rseqc_junction_saturation_plot_Novel_Junctions\.png/, + /rseqc_junction_saturation_plot_Novel_Junctions\.svg/, + /rseqc_junction_saturation_plot_Novel_Junctions\.txt/, + /rseqc_read_distribution_plot-cnt\.pdf/, + /rseqc_read_distribution_plot-cnt\.png/, + /rseqc_read_distribution_plot-cnt\.svg/, + /rseqc_read_distribution_plot-pct\.pdf/, + /rseqc_read_distribution_plot-pct\.png/, + /rseqc_read_distribution_plot-pct\.svg/, + /rseqc_read_distribution_plot\.txt/, + /rseqc_read_dups\.txt/, + /rseqc_read_dups_plot\.pdf/, + /rseqc_read_dups_plot\.svg/, + /rseqc_read_dups_plot\.txt/, + /(salmon|star_rsem)_deseq2_(clustering|pca)-plot\.pdf/, + /(salmon|star_rsem)_deseq2_(clustering|pca)-plot\.png/, + /(salmon|star_rsem)_deseq2_(clustering|pca)-plot\.svg/, + /(salmon|star_rsem)_deseq2_(pca|pca)-plot\.pdf/, + /(salmon|star_rsem)_deseq2_(pca|pca)-plot\.png/, + /(salmon|star_rsem)_deseq2_(pca|pca)-plot\.svg/, + /salmon_plot\.pdf/, + /salmon_plot\.png/, + /salmon_plot\.svg/, + /salmon_plot\.txt/, + /samtools-flagstat-dp_Percentage_of_total\.pdf/, + /samtools-flagstat-dp_Percentage_of_total\.png/, + /samtools-flagstat-dp_Percentage_of_total\.svg/, + /samtools-flagstat-dp_Percentage_of_total\.txt/, + /samtools-flagstat-dp_Read_counts\.pdf/, + /samtools-flagstat-dp_Read_counts\.png/, + /samtools-flagstat-dp_Read_counts\.svg/, + /samtools-flagstat-dp_Read_counts\.txt/, + /samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt\.pdf/, + /samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt\.svg/, + /samtools-idxstats-mapped-reads-plot_Normalised_Counts-log\.pdf/, + /samtools-idxstats-mapped-reads-plot_Normalised_Counts-log\.svg/, + /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt\.pdf/, + /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt\.svg/, + /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log\.pdf/, + /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log\.svg/, + /samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt\.pdf/, + /samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt\.svg/, + /samtools-idxstats-mapped-reads-plot_Raw_Counts-log\.pdf/, + /samtools-idxstats-mapped-reads-plot_Raw_Counts-log\.svg/, + /samtools-stats-dp\.pdf/, + /samtools-stats-dp\.png/, + /samtools-stats-dp\.svg/, + /samtools-stats-dp\.txt/, + /samtools_alignment_plot-cnt\.pdf/, + /samtools_alignment_plot-cnt\.png/, + /samtools_alignment_plot-cnt\.svg/, + /samtools_alignment_plot-pct\.pdf/, + /samtools_alignment_plot-pct\.png/, + /samtools_alignment_plot-pct\.svg/, + /samtools_alignment_plot\.txt/, + /sortmerna-detailed-plot-(cnt|pct)\.(pdf|svg)/, + /sortmerna-detailed-plot\.txt/, + /star_alignment_plot-cnt\.pdf/, + /star_alignment_plot-cnt\.png/, + /star_alignment_plot-cnt\.svg/, + /star_alignment_plot-pct\.pdf/, + /star_alignment_plot-pct\.png/, + /star_alignment_plot-pct\.svg/, + /star_alignment_plot\.txt/, + /(star_rsem|star_salmon)_deseq2_(clustering|pca)-plot(.*)?\.(pdf|png|svg)/, + /star_salmon_deseq2_pca-plot\.(pdf|png|svg)/, + /star_summary_table\.(pdf|png|svg|txt)/, + + // To exclude from deseq2_qc + /RAP1_IAA_30M_REP1\.txt/, + /RAP1_UNINDUCED_REP1\.txt/, + /RAP1_UNINDUCED_REP2\.txt/, + /WT_REP1\.txt/, + /WT_REP2\.txt/, + /deseq2.*/, + + // To exclude from kallisto + /abundance\.(h5|tsv)/, + /kallisto_quant\.log/, + /run_info\.json/, + + // To exclude from salmon quant + /fld\.gz/, + /meta_info\.json/, + /flenDist\.txt/, + /salmon_quant\.log/, + /quant\.genes\.sf/, + /quant\.sf/, + + // To exclude from kallisto|salmon aligners + /(kallisto|salmon)\.merged.*/, + + // To exclude bigwig + /.*\.(forward|reverse)\.bigWig/, + + // To exclude dupradar + /.*_(duprateExpBoxplot|duprateExpDens|expressionHist)\.pdf/, + + // To exclude featurecounts + /.*\.featureCounts\.txt\.summary/, + + // To exclude star salmon + /.*\.Log\.?(final|progress)?\.out/, + + // To exclude Picard Markduplicates metrics + /.*\.markdup\.sorted\.MarkDuplicates\.metrics\.txt/, + + // To exclude Qualimap files + /Junction\sAnalysis\.png/, + /Reads\sGenomic\sOrigin\.png/, + /qualimapReport\.html/, + /rnaseq_qc_results\.txt/, + + // To exclude rseqc + /.*\.DupRate_plot\.(pdf|r)/, + /.*\.inner_distance.*/, + /.*\.junction.*/, + /.*\.(pos|seq)\.DupRate\.xls/, + /.*\.read_distribution\.txt/, + /.*\.splice_(events|junction)\.pdf/, + /.*\.bam_stat\.txt/, + + // To exclude from samtools stats + /.*\.sorted\.bam\.(flagstat|idxstats|stats)/, + + // To exclude from hisat2 + /.*hisat2\.summary/, + + // To exclude from stringtie + /t_data\.ctab/, + /.*\.coverage\.gtf/, + /.*\.gene\.abundance\.txt/, + /.*\.transcripts\.gtf/, + + // To exclude from sortmerna + /.*\.sortmerna\.log/, + + // To exclude log from star rsem + /RAP1_IAA_30M_REP1\.log/, + /RAP1_UNINDUCED_REP1\.log/, + /RAP1_UNINDUCED_REP2\.log/, + /WT_REP1\.log/, + /WT_REP2\.log/, + + // To exclude markdup + /.*\.markdup\.sorted\.bam(\.bai)?/, + + // To exclude trimgalore + /.*\.fastq\.gz_trimming_report\.txt/ + ] +} diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index f2b857136..361315a5a 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -16,7 +16,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -48,7 +48,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index df264b9eb..8b757b1c6 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -16,7 +16,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -48,7 +48,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index c561d7487..3d373840c 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -18,7 +18,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -52,7 +52,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index 9d2d6291d..5d3d876bc 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -16,7 +16,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -48,7 +48,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index 8df873f4a..646381674 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -16,7 +16,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 664d07cc5..804808e18 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -16,7 +16,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -48,7 +48,7 @@ nextflow_pipeline { // path_name_stable: All files + folders in ${params.outdir}/ with a stable name def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS.exclusionRegexesForUnstableFileContents) + def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( From 26737a741c49f5066ea7de2be5b7711fe713b792 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 19 Sep 2024 15:49:05 +0200 Subject: [PATCH 068/100] simplify regexes --- tests/lib/UTILS_PIPELINE.groovy | 214 ++++++-------------------------- 1 file changed, 37 insertions(+), 177 deletions(-) diff --git a/tests/lib/UTILS_PIPELINE.groovy b/tests/lib/UTILS_PIPELINE.groovy index f0074a6cc..f5361ab70 100644 --- a/tests/lib/UTILS_PIPELINE.groovy +++ b/tests/lib/UTILS_PIPELINE.groovy @@ -26,68 +26,19 @@ class UTILS_PIPELINE { /fastqc-status-check-.*\.(pdf|svg)/, /fastqc_adapter_content_plot\.(pdf|png|svg)/, /fastqc_overrepresented_sequences_plot(.*)?\.(pdf|svg)/, - /fastqc_per_base_n_content_plot-1\.pdf/, - /fastqc_per_base_n_content_plot-1\.png/, - /fastqc_per_base_n_content_plot-1\.svg/, - /fastqc_per_base_n_content_plot\.pdf/, - /fastqc_per_base_n_content_plot\.png/, - /fastqc_per_base_n_content_plot\.svg/, - /fastqc_per_base_sequence_quality_plot-1\.pdf/, - /fastqc_per_base_sequence_quality_plot-1\.png/, - /fastqc_per_base_sequence_quality_plot-1\.svg/, - /fastqc_per_base_sequence_quality_plot\.pdf/, - /fastqc_per_base_sequence_quality_plot\.png/, - /fastqc_per_base_sequence_quality_plot\.svg/, - /fastqc_per_sequence_gc_content_plot-1_Counts\.pdf/, - /fastqc_per_sequence_gc_content_plot-1_Counts\.svg/, - /fastqc_per_sequence_gc_content_plot-1_Percentages\.pdf/, - /fastqc_per_sequence_gc_content_plot-1_Percentages\.svg/, - /fastqc_per_sequence_gc_content_plot_Counts\.pdf/, - /fastqc_per_sequence_gc_content_plot_Counts\.svg/, - /fastqc_per_sequence_gc_content_plot_Percentages\.pdf/, - /fastqc_per_sequence_gc_content_plot_Percentages\.svg/, - /fastqc_per_sequence_quality_scores_plot-1\.pdf/, - /fastqc_per_sequence_quality_scores_plot-1\.svg/, - /fastqc_per_sequence_quality_scores_plot\.pdf/, - /fastqc_per_sequence_quality_scores_plot\.svg/, - /fastqc_sequence_counts_plot-1-cnt\.pdf/, - /fastqc_sequence_counts_plot-1-cnt\.svg/, - /fastqc_sequence_counts_plot-1-pct\.pdf/, - /fastqc_sequence_counts_plot-1-pct\.svg/, - /fastqc_sequence_counts_plot-cnt\.pdf/, - /fastqc_sequence_counts_plot-cnt\.svg/, - /fastqc_sequence_counts_plot-pct\.pdf/, - /fastqc_sequence_counts_plot-pct\.svg/, - /fastqc_sequence_duplication_levels_plot-1\.pdf/, - /fastqc_sequence_duplication_levels_plot-1\.svg/, - /fastqc_sequence_duplication_levels_plot\.pdf/, - /fastqc_sequence_duplication_levels_plot\.svg/, - /fastqc_sequence_length_distribution_plot\.pdf/, - /fastqc_sequence_length_distribution_plot\.png/, - /fastqc_sequence_length_distribution_plot\.svg/, - /fastqc_top_overrepresented_sequences_table-1\.pdf/, - /fastqc_top_overrepresented_sequences_table-1\.png/, - /fastqc_top_overrepresented_sequences_table-1\.svg/, - /fastqc_top_overrepresented_sequences_table-1\.txt/, - /fastqc_top_overrepresented_sequences_table\.pdf/, - /fastqc_top_overrepresented_sequences_table\.png/, - /fastqc_top_overrepresented_sequences_table\.svg/, - /fastqc_top_overrepresented_sequences_table\.txt/, - /featurecounts_biotype_plot-cnt\.pdf/, - /featurecounts_biotype_plot-cnt\.svg/, - /featurecounts_biotype_plot-pct\.pdf/, - /featurecounts_biotype_plot-pct\.svg/, - /general_stats_table\.pdf/, - /general_stats_table\.png/, - /general_stats_table\.svg/, + /fastqc_per_base_.*_plot(.*)?\.(pdf|png|svg)/, + /fastqc_per_sequence_.*\.(pdf|svg)/, + /fastqc_sequence_(counts|duplication_levels)_plot(.*)?-(cnt|pct)\.(pdf|svg)/, + /fastqc_sequence_length_distribution_plot\.(pdf|png|svg)/, + /fastqc_top_overrepresented_sequences_table(.*)?\.(pdf|png|svg|txt)/, + /featurecounts_biotype_plot-(cnt|pct)\.(pdf|png|svg)/, + /general_stats_table\.(pdf|png|svg)/, /hisat2_(pe|se)_plot-(cnt|pct)\.(pdf|png|svg)/, /hisat2_pe_plot\.txt/, /hisat2_se_plot.*\.(png|svg)/, /junction_saturation_known\.txt/, /junction_saturation_novel\.txt/, - /kallisto_alignment.*.pdf/, - /kallisto_alignment.*.png/, - /kallisto_alignment.*.svg/, + /kallisto_alignment.*.(pdf|png|svg)/, /kallisto_alignment\.txt/, /multiqc_data\.json/, /multiqc_dupradar-section-plot\.txt/, @@ -104,141 +55,46 @@ class UTILS_PIPELINE { /multiqc_rseqc_read_distribution\.txt/, /multiqc_salmon\.txt/, /(multiqc_)?(salmon|star_salmon|star_rsem)_deseq2_clustering-plot(.*)?\.(pdf|png|txt)/, - /multiqc_salmon_deseq2_pca-plot.*\.txt/, + /multiqc_(salmon|star_salmon)_deseq2_pca-plot.*\.txt/, /multiqc_samtools_flagstat\.txt/, /multiqc_samtools_stats\.txt/, /multiqc_software_versions\.txt/, /multiqc_sortmerna\.txt/, /multiqc_sources\.txt/, /multiqc_star\.txt/, - /multiqc_star_salmon_deseq2_pca-plot\.txt/, - /picard_deduplication-cnt\.pdf/, - /picard_deduplication-cnt\.png/, - /picard_deduplication-cnt\.svg/, - /picard_deduplication-pct\.pdf/, - /picard_deduplication-pct\.png/, - /picard_deduplication-pct\.svg/, + /picard_deduplication-(cnt|pct)\.(pdf|png|svg)/, /picard_deduplication\.txt/, - /qualimap_gene_coverage_profile_Counts\.pdf/, - /qualimap_gene_coverage_profile_Counts\.svg/, - /qualimap_gene_coverage_profile_Normalised\.pdf/, - /qualimap_gene_coverage_profile_Normalised\.svg/, - /qualimap_genomic_origin-cnt\.pdf/, - /qualimap_genomic_origin-cnt\.png/, - /qualimap_genomic_origin-cnt\.svg/, - /qualimap_genomic_origin-pct\.pdf/, - /qualimap_genomic_origin-pct\.png/, - /qualimap_genomic_origin-pct\.svg/, + /qualimap_gene_coverage_profile_Counts\.(pdf|svg)/, + /qualimap_gene_coverage_profile_Normalised\.(pdf|svg)/, + /qualimap_genomic_origin-(cnt|pct)\.(pdf|png|svg)/, /qualimap_genomic_origin\.txt/, /qualimap_rnaseq_genome_results\.txt/, /rsem_assignment_plot\.txt/, /rsem_assignment_plot-(cnt|pct)\.(pdf|png|svg)/, /rsem_multimapping_rates\.(pdf|svg|txt)/, - /rseqc_bam_stat\.pdf/, - /rseqc_bam_stat\.png/, - /rseqc_bam_stat\.svg/, - /rseqc_bam_stat\.txt/, - /rseqc_infer_experiment_plot\.pdf/, - /rseqc_infer_experiment_plot\.svg/, - /rseqc_inner_distance\.txt/, - /rseqc_inner_distance_plot_Counts\.pdf/, - /rseqc_inner_distance_plot_Counts\.png/, - /rseqc_inner_distance_plot_Counts\.svg/, - /rseqc_inner_distance_plot_Counts\.txt/, - /rseqc_inner_distance_plot_Percentages\.pdf/, - /rseqc_inner_distance_plot_Percentages\.png/, - /rseqc_inner_distance_plot_Percentages\.svg/, - /rseqc_inner_distance_plot_Percentages\.txt/, - /rseqc_junction_annotation_junctions_plot_Events-cnt\.pdf/, - /rseqc_junction_annotation_junctions_plot_Events-cnt\.png/, - /rseqc_junction_annotation_junctions_plot_Events-cnt\.svg/, - /rseqc_junction_annotation_junctions_plot_Events-pct\.pdf/, - /rseqc_junction_annotation_junctions_plot_Events-pct\.png/, - /rseqc_junction_annotation_junctions_plot_Events-pct\.svg/, - /rseqc_junction_annotation_junctions_plot_Events\.txt/, - /rseqc_junction_annotation_junctions_plot_Junctions-cnt\.pdf/, - /rseqc_junction_annotation_junctions_plot_Junctions-cnt\.png/, - /rseqc_junction_annotation_junctions_plot_Junctions-cnt\.svg/, - /rseqc_junction_annotation_junctions_plot_Junctions-pct\.pdf/, - /rseqc_junction_annotation_junctions_plot_Junctions-pct\.png/, - /rseqc_junction_annotation_junctions_plot_Junctions-pct\.svg/, - /rseqc_junction_annotation_junctions_plot_Junctions\.txt/, - /rseqc_junction_saturation_all\.txt/, - /rseqc_junction_saturation_plot_All_Junctions\.pdf/, - /rseqc_junction_saturation_plot_All_Junctions\.png/, - /rseqc_junction_saturation_plot_All_Junctions\.svg/, - /rseqc_junction_saturation_plot_All_Junctions\.txt/, - /rseqc_junction_saturation_plot_Known_Junctions\.pdf/, - /rseqc_junction_saturation_plot_Known_Junctions\.png/, - /rseqc_junction_saturation_plot_Known_Junctions\.svg/, - /rseqc_junction_saturation_plot_Known_Junctions\.txt/, - /rseqc_junction_saturation_plot_Novel_Junctions\.pdf/, - /rseqc_junction_saturation_plot_Novel_Junctions\.png/, - /rseqc_junction_saturation_plot_Novel_Junctions\.svg/, - /rseqc_junction_saturation_plot_Novel_Junctions\.txt/, - /rseqc_read_distribution_plot-cnt\.pdf/, - /rseqc_read_distribution_plot-cnt\.png/, - /rseqc_read_distribution_plot-cnt\.svg/, - /rseqc_read_distribution_plot-pct\.pdf/, - /rseqc_read_distribution_plot-pct\.png/, - /rseqc_read_distribution_plot-pct\.svg/, - /rseqc_read_distribution_plot\.txt/, + /rseqc_bam_stat\.(pdf|png|svg|txt)/, + /rseqc_infer_experiment_plot\.(pdf|svg)/, + /rseqc_inner_.*/, + /rseqc_junction_.*/, + /rseqc_read_distribution_.*/, /rseqc_read_dups\.txt/, - /rseqc_read_dups_plot\.pdf/, - /rseqc_read_dups_plot\.svg/, + /rseqc_read_dups_plot\.(pdf|svg)/, /rseqc_read_dups_plot\.txt/, - /(salmon|star_rsem)_deseq2_(clustering|pca)-plot\.pdf/, - /(salmon|star_rsem)_deseq2_(clustering|pca)-plot\.png/, - /(salmon|star_rsem)_deseq2_(clustering|pca)-plot\.svg/, - /(salmon|star_rsem)_deseq2_(pca|pca)-plot\.pdf/, - /(salmon|star_rsem)_deseq2_(pca|pca)-plot\.png/, - /(salmon|star_rsem)_deseq2_(pca|pca)-plot\.svg/, - /salmon_plot\.pdf/, - /salmon_plot\.png/, - /salmon_plot\.svg/, - /salmon_plot\.txt/, - /samtools-flagstat-dp_Percentage_of_total\.pdf/, - /samtools-flagstat-dp_Percentage_of_total\.png/, - /samtools-flagstat-dp_Percentage_of_total\.svg/, - /samtools-flagstat-dp_Percentage_of_total\.txt/, - /samtools-flagstat-dp_Read_counts\.pdf/, - /samtools-flagstat-dp_Read_counts\.png/, - /samtools-flagstat-dp_Read_counts\.svg/, - /samtools-flagstat-dp_Read_counts\.txt/, - /samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt\.pdf/, - /samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt\.svg/, - /samtools-idxstats-mapped-reads-plot_Normalised_Counts-log\.pdf/, - /samtools-idxstats-mapped-reads-plot_Normalised_Counts-log\.svg/, - /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt\.pdf/, - /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt\.svg/, - /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log\.pdf/, - /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log\.svg/, - /samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt\.pdf/, - /samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt\.svg/, - /samtools-idxstats-mapped-reads-plot_Raw_Counts-log\.pdf/, - /samtools-idxstats-mapped-reads-plot_Raw_Counts-log\.svg/, - /samtools-stats-dp\.pdf/, - /samtools-stats-dp\.png/, - /samtools-stats-dp\.svg/, - /samtools-stats-dp\.txt/, - /samtools_alignment_plot-cnt\.pdf/, - /samtools_alignment_plot-cnt\.png/, - /samtools_alignment_plot-cnt\.svg/, - /samtools_alignment_plot-pct\.pdf/, - /samtools_alignment_plot-pct\.png/, - /samtools_alignment_plot-pct\.svg/, - /samtools_alignment_plot\.txt/, + /(salmon|star_rsem)_deseq2_(clustering|pca)-plot\.(pdf|png|svg)/, + /(salmon|star_rsem)_deseq2_(pca|pca)-plot\.(pdf|png|svg)/, + /salmon_plot\.(pdf|png|svg|txt)/, + /samtools-flagstat.*/, + /samtools-idxstats-mapped-reads-plot_Normalised_Counts-(cnt|pct)\.(pdf|svg)/, + /samtools-idxstats-mapped-reads-plot_Normalised_Counts-log\.(pdf|svg)/, + /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-(cnt|pct)\.(pdf|svg)/, + /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log\.(pdf|svg)/, + /samtools-idxstats-mapped-reads-plot_Raw_Counts-(cnt|pct)\.(pdf|svg)/, + /samtools-idxstats-mapped-reads-plot_Raw_Counts-log\.(pdf|svg)/, + /samtools-stats-dp\.(pdf|png|svg|txt)/, + /(samtools|star)_alignment_plot.*/, /sortmerna-detailed-plot-(cnt|pct)\.(pdf|svg)/, /sortmerna-detailed-plot\.txt/, - /star_alignment_plot-cnt\.pdf/, - /star_alignment_plot-cnt\.png/, - /star_alignment_plot-cnt\.svg/, - /star_alignment_plot-pct\.pdf/, - /star_alignment_plot-pct\.png/, - /star_alignment_plot-pct\.svg/, - /star_alignment_plot\.txt/, /(star_rsem|star_salmon)_deseq2_(clustering|pca)-plot(.*)?\.(pdf|png|svg)/, - /star_salmon_deseq2_pca-plot\.(pdf|png|svg)/, /star_summary_table\.(pdf|png|svg|txt)/, // To exclude from deseq2_qc @@ -265,11 +121,15 @@ class UTILS_PIPELINE { // To exclude from kallisto|salmon aligners /(kallisto|salmon)\.merged.*/, + // To exclude from star_rsem + /.*.(genes|isoforms)\.results/, + /.*.(cnt|model|theta)/, + // To exclude bigwig /.*\.(forward|reverse)\.bigWig/, // To exclude dupradar - /.*_(duprateExpBoxplot|duprateExpDens|expressionHist)\.pdf/, + /.*_(duprateExpBoxplot|duprateExpDens|expressionHist)\.(pdf|png|svg)/, // To exclude featurecounts /.*\.featureCounts\.txt\.summary/, @@ -292,7 +152,7 @@ class UTILS_PIPELINE { /.*\.junction.*/, /.*\.(pos|seq)\.DupRate\.xls/, /.*\.read_distribution\.txt/, - /.*\.splice_(events|junction)\.pdf/, + /.*\.splice_(events|junction)\.(pdf|png|svg)/, /.*\.bam_stat\.txt/, // To exclude from samtools stats From 3172eaa76d7382b429ef8abc3c81a00943db3d83 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 19 Sep 2024 16:14:15 +0200 Subject: [PATCH 069/100] fix regexes --- tests/lib/UTILS_PIPELINE.groovy | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/lib/UTILS_PIPELINE.groovy b/tests/lib/UTILS_PIPELINE.groovy index f5361ab70..01bf858fe 100644 --- a/tests/lib/UTILS_PIPELINE.groovy +++ b/tests/lib/UTILS_PIPELINE.groovy @@ -28,10 +28,10 @@ class UTILS_PIPELINE { /fastqc_overrepresented_sequences_plot(.*)?\.(pdf|svg)/, /fastqc_per_base_.*_plot(.*)?\.(pdf|png|svg)/, /fastqc_per_sequence_.*\.(pdf|svg)/, - /fastqc_sequence_(counts|duplication_levels)_plot(.*)?-(cnt|pct)\.(pdf|svg)/, + /fastqc_sequence_(counts|duplication_levels)_plot(.*)?\.(pdf|svg)/, /fastqc_sequence_length_distribution_plot\.(pdf|png|svg)/, /fastqc_top_overrepresented_sequences_table(.*)?\.(pdf|png|svg|txt)/, - /featurecounts_biotype_plot-(cnt|pct)\.(pdf|png|svg)/, + /featurecounts_biotype_plot-(cnt|pct)\.(pdf|svg)/, /general_stats_table\.(pdf|png|svg)/, /hisat2_(pe|se)_plot-(cnt|pct)\.(pdf|png|svg)/, /hisat2_pe_plot\.txt/, From bc193dfde41e649e62307746ef95ecc940998c24 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Thu, 19 Sep 2024 11:13:38 -0400 Subject: [PATCH 070/100] Merge conflcits --- CHANGELOG.md | 28 ++ CITATIONS.md | 8 + README.md | 1 + docs/images/bracken-top-n-plot.png | Bin 0 -> 55992 bytes docs/images/nf-core-rnaseq_metro_map_grey.png | Bin 291676 -> 302024 bytes docs/images/nf-core-rnaseq_metro_map_grey.svg | 414 ++++++++++-------- docs/output.md | 22 +- docs/usage.md | 8 + modules.json | 13 +- .../nf-core/bracken/bracken/environment.yml | 7 + modules/nf-core/bracken/bracken/main.nf | 55 +++ modules/nf-core/bracken/bracken/meta.yml | 51 +++ .../nf-core/bracken/bracken/nextflow.config | 13 + .../bracken/bracken/tests/genus_test.config | 5 + .../bracken/bracken/tests/main.nf.test | 167 +++++++ .../bracken/bracken/tests/main.nf.test.snap | 210 +++++++++ .../bracken/bracken/tests/nextflow.config | 5 + .../nf-core/bracken/bracken/tests/tags.yml | 2 + .../nf-core/hisat2/align/hisat2-align.diff | 56 +++ modules/nf-core/hisat2/align/main.nf | 7 +- .../nf-core/kraken2/kraken2/environment.yml | 9 + modules/nf-core/kraken2/kraken2/main.nf | 85 ++++ modules/nf-core/kraken2/kraken2/meta.yml | 78 ++++ .../nf-core/kraken2/kraken2/nextflow.config | 15 + .../kraken2/kraken2/tests/main.nf.test | 143 ++++++ .../kraken2/kraken2/tests/main.nf.test.snap | 74 ++++ .../nf-core/kraken2/kraken2/tests/tags.yml | 3 + nextflow.config | 5 + nextflow_schema.json | 32 ++ subworkflows/local/align_star/nextflow.config | 2 +- .../utils_nfcore_rnaseq_pipeline/main.nf | 43 ++ .../rnaseq/assets/multiqc/multiqc_config.yml | 8 + workflows/rnaseq/main.nf | 59 ++- workflows/rnaseq/nextflow.config | 2 + 34 files changed, 1429 insertions(+), 201 deletions(-) create mode 100644 docs/images/bracken-top-n-plot.png create mode 100644 modules/nf-core/bracken/bracken/environment.yml create mode 100644 modules/nf-core/bracken/bracken/main.nf create mode 100644 modules/nf-core/bracken/bracken/meta.yml create mode 100644 modules/nf-core/bracken/bracken/nextflow.config create mode 100644 modules/nf-core/bracken/bracken/tests/genus_test.config create mode 100644 modules/nf-core/bracken/bracken/tests/main.nf.test create mode 100644 modules/nf-core/bracken/bracken/tests/main.nf.test.snap create mode 100644 modules/nf-core/bracken/bracken/tests/nextflow.config create mode 100644 modules/nf-core/bracken/bracken/tests/tags.yml create mode 100644 modules/nf-core/hisat2/align/hisat2-align.diff create mode 100644 modules/nf-core/kraken2/kraken2/environment.yml create mode 100644 modules/nf-core/kraken2/kraken2/main.nf create mode 100644 modules/nf-core/kraken2/kraken2/meta.yml create mode 100644 modules/nf-core/kraken2/kraken2/nextflow.config create mode 100644 modules/nf-core/kraken2/kraken2/tests/main.nf.test create mode 100644 modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap create mode 100644 modules/nf-core/kraken2/kraken2/tests/tags.yml diff --git a/CHANGELOG.md b/CHANGELOG.md index 916c78035..e9c90c34c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,8 +7,36 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Enhancements & fixes +- [PR #1351](https://github.com/nf-core/rnaseq/pull/1351) - Adding Kraken2/Bracken on unaligned reads as an additional quality control step to detect sample contamination - [PR #1186](https://github.com/nf-core/rnaseq/pull/1186) - Bump pipeline version to 3.16.0dev +### Parameters + +| Old parameter | New parameter | +| ------------- | --------------------------- | +| | `--contaminant_screening` | +| | `--kraken_db` | +| | `--save_kraken_assignments` | +| | `--save_kraken_unassigned` | +| | `--bracken_precision` | + +> **NB:** Parameter has been **updated** if both old and new parameter information is present. +> **NB:** Parameter has been **added** if just the new parameter information is present. +> **NB:** Parameter has been **removed** if new parameter information isn't present. + +### Software dependencies + +| Dependency | Old version | New version | +| ---------- | ----------- | ----------- | +| `Kraken2` | ----------- | 2.1.3 | +| `Bracken` | ----------- | 2.9 | + +> **NB:** Dependency has been **updated** if both old and new version information is present. +> +> **NB:** Dependency has been **added** if just the new version information is present. +> +> **NB:** Dependency has been **removed** if new version information isn't present. + ## [[3.15.1](https://github.com/nf-core/rnaseq/releases/tag/3.15.1)] - 2024-09-16 ### Enhancements & fixes diff --git a/CITATIONS.md b/CITATIONS.md index 48a60b8e4..5eaeea7f8 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -16,6 +16,10 @@ > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824. +- [Bracken](https://doi.org/10.7717/peerj-cs.104) + + > Lu, J., Breitwieser, F. P., Thielen, P., & Salzberg, S. L. (2017). Bracken: estimating species abundance in metagenomics data. PeerJ. Computer Science, 3(e104), e104. https://doi.org/10.7717/peerj-cs.104 + - [fastp](https://www.ncbi.nlm.nih.gov/pubmed/30423086/) > Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PubMed PMID: 30423086; PubMed Central PMCID: PMC6129281. @@ -38,6 +42,10 @@ > Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4. Epub 2019 Aug 2. PubMed PMID: 31375807. +- [Kraken2](https://doi.org/10.1186/s13059-019-1891-0) + + > Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. https://doi.org/10.1186/s13059-019-1891-0 + - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. diff --git a/README.md b/README.md index c5f58478e..01da6cf8b 100644 --- a/README.md +++ b/README.md @@ -46,6 +46,7 @@ 3. [`dupRadar`](https://bioconductor.org/packages/release/bioc/html/dupRadar.html) 4. [`Preseq`](http://smithlabresearch.org/software/preseq/) 5. [`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html) + 6. [`Kraken2`](https://ccb.jhu.edu/software/kraken2/) -> [`Bracken`](https://ccb.jhu.edu/software/bracken/) on unaligned sequences; _optional_ 15. Pseudoalignment and quantification ([`Salmon`](https://combine-lab.github.io/salmon/) or ['Kallisto'](https://pachterlab.github.io/kallisto/); _optional_) 16. 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zT4VS)c7-p=`vpj)6WOo_N(GD6S;)@tIu_gRP10C6DkM*U`y$_^hd;DnblzW;+w3^h z7I=J)fRq+1*`uWS9jpu!$aIk6gsY`12QA}f6_u2XOiWHp8tsx&S6N*>jbsvDH@2}w zoc`2z+GG&iMZhHaW=8`fqcE!X4gxcGf4xHKiu%GKJ5S$$k}Co=Ah`>}PiD=n#gSFd z=6^G|PrrVlO}`B3UUn6i`xpP|!vO|@kbvVE#uNrT+ts95_RDMWwhO-Tn#L}VI|uvF zL#wE)9B4S)iQQ6ZSLD3lwD7LIfpX&EQgU7dmW}D z6s18dq29vdU0BVNu!EHki)cn49ynmopcv;bFHhcSB{8vQ4U^jHYijNmsZdlUQhLML$UeQn2c)r4`O~;De8y=j?d&y$W{&E0ugOSSDc3qxjDB%) zA%`(syEYcZ7s-f4?aP0E_T{-1v#sR%vnC;gv)Q_*XJ?0^1zv)}*zihch)nZG|azJKw5 zeqN$6G_E_T`R6Zp%3F8W6#xAERrBwQ|L5nAd;b3d{;yAC7)rzndwZs`gKM Ki(?n9_xUg9^6Opz diff --git a/docs/images/nf-core-rnaseq_metro_map_grey.svg b/docs/images/nf-core-rnaseq_metro_map_grey.svg index 7b55ae7e5..c36c3e839 100644 --- a/docs/images/nf-core-rnaseq_metro_map_grey.svg +++ b/docs/images/nf-core-rnaseq_metro_map_grey.svg @@ -7,7 +7,7 @@ viewBox="0 0 646.4851 269.92565" version="1.1" id="svg8" - inkscape:version="1.3.2 (1:1.3.2+202311252150+091e20ef0f)" + inkscape:version="1.3.2 (091e20e, 2023-11-25)" sodipodi:docname="nf-core-rnaseq_metro_map_grey.svg" inkscape:export-filename="nf-core-rnaseq_metro_map_grey.png" inkscape:export-xdpi="89" @@ -2775,24 +2775,39 @@ id="stop23-7" />RSeQC(multiple modules)Kraken2/Bracken5RSeQC(multiple modules)PreseqPreseqdupRadarDESeq2(PCA only)MultiQCQualimaprnaseqHTMLHTMLHTMLdupRadarMultiQCQualimaprnaseqDESeq2(PCA only)MultiQC - DESeq2 sample similarity plot

+### Kraken2/Bracken + +
+Output files + +- `/contaminants/kraken2/kraken_reports` + - `*.kraken2.report.txt`: Classification of unaligned reads in the Kraken report format. See the [kraken2 manual](https://github.com/DerrickWood/kraken2/wiki/Manual#output-formats) for more details + - `*.classified*.fastq.gz` If `--save_kraken_alignments`, outputs fastq file for each sample with each classified read annotated with taxonomic identification from Kraken2. + - `*.unclassified*.fastq.gz` If `save_kraken_unassigned`, outputs fastq file with all reads that were not classified by Kraken2. +- `/contaminants/bracken/` + - `*.kraken2.report_bracken.txt`: Kraken-style reports of the Bracken abundance estimate results. See the [kraken2 manual](https://github.com/DerrickWood/kraken2/wiki/Manual#output-formats) for more details. + - `*.tsv` Summary of estimated reads for each taxon member at the given classification level and what corrections were made from Kraken2. + +
+ +[Kraken2](https://ccb.jhu.edu/software/kraken2/) is a taxonomic classification tool that uses k-mer matches paired with a lowest common ancestory (LCA) algorithm to classify species reads. [Bracken](https://ccb.jhu.edu/software/bracken/) is a statistical method to generate abundance estimates based off of the Kraken2 output. These algorithms are run on unaligned sequences to detect potential contamination of samples. MultiQC reports the top 5 taxon members detected at the level of classification used for Bracken, with toggles available for higher taxonomic levels. If Bracken is skipped, MultiQC will report the top 5 species detected by Kraken2. + +![MultiQC - Bracken top species plot](images/bracken-top-n-plot.png) + ### MultiQC
@@ -675,7 +695,7 @@ Results generated by MultiQC collate pipeline QC from supported tools i.e. FastQ ### Pseudoalignment -The principal output files are the same between Salmon and Kallsto: +The principal output files are the same between Salmon and Kallisto:
Output files diff --git a/docs/usage.md b/docs/usage.md index b613ab79d..cd42a399b 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -296,6 +296,14 @@ Notes: By default, the input GTF file will be filtered to ensure that sequence names correspond to those in the genome fasta file, and to remove rows with empty transcript identifiers. Filtering can be bypassed completely where you are confident it is not necessary, using the `--skip_gtf_filter` parameter. If you just want to skip the 'transcript_id' checking component of the GTF filtering script used in the pipeline this can be disabled specifically using the `--skip_gtf_transcript_filter` parameter. +## Contamination screening options + +The pipeline provides the option to scan unaligned reads for contamination from other species using [Kraken2](https://ccb.jhu.edu/software/kraken2/), with the possibility of applying corrections from [Bracken](https://ccb.jhu.edu/software/bracken/). Since running Bracken is not computationally expensive, we recommend always using it to refine the abundance estimates generated by Kraken2. + +It is important to note that the accuracy of Kraken2 is [highly dependent on the database](https://doi.org/10.1099/mgen.0.000949) used. Specifically, it is [crucial](https://doi.org/10.1128/mbio.01607-23) to ensure that the host genome is included in the database. If you are particularly concerned about certain contaminants, it may be beneficial to use a smaller, more focused database containing primarily those contaminants instead of the full standard database. Various pre-built databases [are available for download](https://benlangmead.github.io/aws-indexes/k2), and instructions for building a custom database can be found in the [Kraken2 documentation](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown). Additionally, genomes of contaminants detected in previous sequencing experiments are available on the [OpenContami website](https://openlooper.hgc.jp/opencontami/help/help_oct.php). + +While Kraken2 is capable of detecting low-abundance contaminants in a sample, false positives can occur. Therefore, if only a very small number of reads from a contaminating species are detected, these results should be interpreted with caution. + ## Running the pipeline The typical command for running the pipeline is as follows: diff --git a/modules.json b/modules.json index 30090ab26..4c9ba76f1 100644 --- a/modules.json +++ b/modules.json @@ -15,6 +15,11 @@ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, + "bracken/bracken": { + "branch": "master", + "git_sha": "c214fad97b328eb6d6233f779be9ba44814a9136", + "installed_by": ["modules"] + }, "cat/fastq": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", @@ -68,7 +73,8 @@ "hisat2/align": { "branch": "master", "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", - "installed_by": ["fastq_align_hisat2"] + "installed_by": ["fastq_align_hisat2"], + "patch": "modules/nf-core/hisat2/align/hisat2-align.diff" }, "hisat2/build": { "branch": "master", @@ -90,6 +96,11 @@ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules", "quantify_pseudo_alignment"] }, + "kraken2/kraken2": { + "branch": "master", + "git_sha": "a13d5d945742a60bbef6e5c177e81cda540f75dc", + "installed_by": ["modules"] + }, "multiqc": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", diff --git a/modules/nf-core/bracken/bracken/environment.yml b/modules/nf-core/bracken/bracken/environment.yml new file mode 100644 index 000000000..6eb5b1b9a --- /dev/null +++ b/modules/nf-core/bracken/bracken/environment.yml @@ -0,0 +1,7 @@ +name: bracken_bracken +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::bracken=2.9" diff --git a/modules/nf-core/bracken/bracken/main.nf b/modules/nf-core/bracken/bracken/main.nf new file mode 100644 index 000000000..e3d32fb21 --- /dev/null +++ b/modules/nf-core/bracken/bracken/main.nf @@ -0,0 +1,55 @@ +process BRACKEN_BRACKEN { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bracken:2.9--py38h2494328_0': + 'biocontainers/bracken:2.9--py38h2494328_0' }" + + input: + tuple val(meta), path(kraken_report) + path database + + output: + tuple val(meta), path(bracken_report) , emit: reports + tuple val(meta), path(bracken_kraken_style_report), emit: txt + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: "" + def prefix = task.ext.prefix ?: "${meta.id}" + bracken_report = "${prefix}.tsv" + bracken_kraken_style_report = "${prefix}.kraken2.report_bracken.txt" + """ + bracken \\ + ${args} \\ + -d '${database}' \\ + -i '${kraken_report}' \\ + -o '${bracken_report}' \\ + -w '${bracken_kraken_style_report}' + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bracken: \$(echo \$(bracken -v) | cut -f2 -d'v') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + bracken_report = "${prefix}.tsv" + bracken_kraken_style_report = "${prefix}.kraken2.report_bracken.txt" + """ + touch ${prefix}.tsv + touch ${bracken_kraken_style_report} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bracken: \$(echo \$(bracken -v) | cut -f2 -d'v') + END_VERSIONS + """ +} diff --git a/modules/nf-core/bracken/bracken/meta.yml b/modules/nf-core/bracken/bracken/meta.yml new file mode 100644 index 000000000..b7ff4489f --- /dev/null +++ b/modules/nf-core/bracken/bracken/meta.yml @@ -0,0 +1,51 @@ +name: bracken_bracken +description: Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken. +keywords: + - bracken + - metagenomics + - abundance + - kraken2 +tools: + - bracken: + description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. + homepage: https://ccb.jhu.edu/software/bracken/ + documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual + tool_dev_url: https://github.com/jenniferlu717/Bracken + doi: "10.7717/peerj-cs.104" + licence: ["GPL v3"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - kraken_report: + type: file + description: TSV file with six columns coming from kraken2 output + pattern: "*.{tsv}" + - database: + type: file + description: Directory containing the kraken2/Bracken files for analysis + pattern: "*" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - reports: + type: file + description: TSV output report of the re-estimated abundances + pattern: "*.{tsv}" + - txt: + type: file + description: TXT file of bracken corrected results of Kraken2 report output + pattern: "*.txt" +authors: + - "@Midnighter" +maintainers: + - "@Midnighter" diff --git a/modules/nf-core/bracken/bracken/nextflow.config b/modules/nf-core/bracken/bracken/nextflow.config new file mode 100644 index 000000000..975a9793a --- /dev/null +++ b/modules/nf-core/bracken/bracken/nextflow.config @@ -0,0 +1,13 @@ +if (!params.skip_alignment && !params.skip_qc) { + if (params.contaminant_screening == 'kraken2_bracken') { + process { + withName: 'BRACKEN' { + ext.args = "-l ${params.bracken_precision}" + publishDir = [ + path: { "${params.outdir}/${params.aligner}/contaminants/bracken" }, + mode: params.publish_dir_mode + ] + } + } + } +} \ No newline at end of file diff --git a/modules/nf-core/bracken/bracken/tests/genus_test.config b/modules/nf-core/bracken/bracken/tests/genus_test.config new file mode 100644 index 000000000..bc5f63ae0 --- /dev/null +++ b/modules/nf-core/bracken/bracken/tests/genus_test.config @@ -0,0 +1,5 @@ +process { + withName: BRACKEN_BRACKEN { + ext.args = "-l G -t 10 -r 150" + } +} diff --git a/modules/nf-core/bracken/bracken/tests/main.nf.test b/modules/nf-core/bracken/bracken/tests/main.nf.test new file mode 100644 index 000000000..9d2105ded --- /dev/null +++ b/modules/nf-core/bracken/bracken/tests/main.nf.test @@ -0,0 +1,167 @@ +nextflow_process { + + name "Test Process BRACKEN_BRACKEN" + script "../main.nf" + process "BRACKEN_BRACKEN" + + tag "modules" + tag "modules_nfcore" + tag "bracken" + tag "bracken/bracken" + tag "kraken2/kraken2" + tag "untar" + + setup { + run ("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = [[],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2_bracken.tar.gz', checkIfExists: true)] + """ + } + } + } + + test("sarscov2 - single-end - fastq") { + + config "./nextflow.config" + + setup { + run("KRAKEN2_KRAKEN2") { + script "../../../kraken2/kraken2/main.nf" + process { + """ + input[0] = [[id: 'test', single_end: true], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + input[1] = UNTAR.out.untar.map{it[1]} + input[2] = false + input[3] = false + """ + } + } + } + + when { + process { + """ + input[0] = KRAKEN2_KRAKEN2.out.report + input[1] = UNTAR.out.untar.map{it[1]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - paired-end - fastq - genus config") { + + config "./genus_test.config" + + setup { + run("KRAKEN2_KRAKEN2") { + script "../../../kraken2/kraken2/main.nf" + process { + """ + input[0] = [ + [id: 'test', single_end: false], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ] + input[1] = UNTAR.out.untar.map{it[1]} + input[2] = false + input[3] = false + """ + } + } + } + + when { + process { + """ + input[0] = KRAKEN2_KRAKEN2.out.report + input[1] = UNTAR.out.untar.map{it[1]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - paired-end - fastq") { + + config "./nextflow.config" + + setup { + run("KRAKEN2_KRAKEN2") { + script "../../../kraken2/kraken2/main.nf" + process { + """ + input[0] = [ + [id: 'test', single_end: false], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ] + input[1] = UNTAR.out.untar.map{it[1]} + input[2] = false + input[3] = false + """ + } + } + } + + when { + process { + """ + input[0] = KRAKEN2_KRAKEN2.out.report + input[1] = UNTAR.out.untar.map{it[1]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - stub - fastq") { + + options "-stub" + + when { + process { + """ + input[0] = [[id: 'test'],file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true)] + input[1] = UNTAR.out.untar.map{it[1]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/bracken/bracken/tests/main.nf.test.snap b/modules/nf-core/bracken/bracken/tests/main.nf.test.snap new file mode 100644 index 000000000..c97a4c71b --- /dev/null +++ b/modules/nf-core/bracken/bracken/tests/main.nf.test.snap @@ -0,0 +1,210 @@ +{ + "sarscov2 - single-end - fastq": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.tsv:md5,4a21ae14ff8a0311d55f139af5247838" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.kraken2.report_bracken.txt:md5,ca0fbeedc4353b5fdd081688823a33df" + ] + ], + "2": [ + "versions.yml:md5,599fbbf4c1cd5851022a98788f2afdba" + ], + "reports": [ + [ + { + "id": "test", + "single_end": true + }, + "test.tsv:md5,4a21ae14ff8a0311d55f139af5247838" + ] + ], + "txt": [ + [ + { + "id": "test", + "single_end": true + }, + "test.kraken2.report_bracken.txt:md5,ca0fbeedc4353b5fdd081688823a33df" + ] + ], + "versions": [ + "versions.yml:md5,599fbbf4c1cd5851022a98788f2afdba" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-06T11:35:03.995620397" + }, + "sarscov2 - paired-end - fastq - genus config": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,f609b09d6edb5ebc1ea1435d1dd46cde" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.kraken2.report_bracken.txt:md5,2ce58814420a3690da1f08e10e8d3a30" + ] + ], + "2": [ + "versions.yml:md5,599fbbf4c1cd5851022a98788f2afdba" + ], + "reports": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,f609b09d6edb5ebc1ea1435d1dd46cde" + ] + ], + "txt": [ + [ + { + "id": "test", + "single_end": false + }, + "test.kraken2.report_bracken.txt:md5,2ce58814420a3690da1f08e10e8d3a30" + ] + ], + "versions": [ + "versions.yml:md5,599fbbf4c1cd5851022a98788f2afdba" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-06T12:13:33.399680181" + }, + "sarscov2 - paired-end - fastq": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,4a21ae14ff8a0311d55f139af5247838" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.kraken2.report_bracken.txt:md5,ca0fbeedc4353b5fdd081688823a33df" + ] + ], + "2": [ + "versions.yml:md5,599fbbf4c1cd5851022a98788f2afdba" + ], + "reports": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,4a21ae14ff8a0311d55f139af5247838" + ] + ], + "txt": [ + [ + { + "id": "test", + "single_end": false + }, + "test.kraken2.report_bracken.txt:md5,ca0fbeedc4353b5fdd081688823a33df" + ] + ], + "versions": [ + "versions.yml:md5,599fbbf4c1cd5851022a98788f2afdba" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-06T12:09:15.465609745" + }, + "sarscov2 - stub - fastq": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.kraken2.report_bracken.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,599fbbf4c1cd5851022a98788f2afdba" + ], + "reports": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "txt": [ + [ + { + "id": "test" + }, + "test.kraken2.report_bracken.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,599fbbf4c1cd5851022a98788f2afdba" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-06T11:35:42.965471207" + } +} \ No newline at end of file diff --git a/modules/nf-core/bracken/bracken/tests/nextflow.config b/modules/nf-core/bracken/bracken/tests/nextflow.config new file mode 100644 index 000000000..b550b7489 --- /dev/null +++ b/modules/nf-core/bracken/bracken/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: BRACKEN_BRACKEN { + ext.args = "-l S -t 10 -r 150" + } +} diff --git a/modules/nf-core/bracken/bracken/tests/tags.yml b/modules/nf-core/bracken/bracken/tests/tags.yml new file mode 100644 index 000000000..6a2cbd384 --- /dev/null +++ b/modules/nf-core/bracken/bracken/tests/tags.yml @@ -0,0 +1,2 @@ +bracken/bracken: + - "modules/nf-core/bracken/bracken/**" diff --git a/modules/nf-core/hisat2/align/hisat2-align.diff b/modules/nf-core/hisat2/align/hisat2-align.diff new file mode 100644 index 000000000..6086520f6 --- /dev/null +++ b/modules/nf-core/hisat2/align/hisat2-align.diff @@ -0,0 +1,56 @@ +Changes in module 'nf-core/hisat2/align' +--- modules/nf-core/hisat2/align/main.nf ++++ modules/nf-core/hisat2/align/main.nf +@@ -36,7 +36,7 @@ + ss = "$splicesites" ? "--known-splicesite-infile $splicesites" : '' + def seq_center = params.seq_center ? "--rg-id ${prefix} --rg SM:$prefix --rg CN:${params.seq_center.replaceAll('\\s','_')}" : "--rg-id ${prefix} --rg SM:$prefix" + if (meta.single_end) { +- def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' ++ def unaligned = params.save_unaligned || params.contaminant_screening ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' + """ + INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'` + hisat2 \\ +@@ -58,7 +58,7 @@ + END_VERSIONS + """ + } else { +- def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' ++ def unaligned = params.save_unaligned || params.contaminant_screening ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' + """ + INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'` + hisat2 \\ +@@ -93,7 +93,7 @@ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" +- def unaligned = params.save_unaligned ? "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz \n echo '' | gzip > ${prefix}.unmapped_2.fastq.gz" : '' ++ def unaligned = params.save_unaligned || params.contaminant_screening ? "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz \n echo '' | gzip > ${prefix}.unmapped_2.fastq.gz" : '' + def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + """ + ${unaligned} + +--- modules/nf-core/hisat2/align/tests/main.nf.test ++++ modules/nf-core/hisat2/align/tests/main.nf.test +@@ -3,12 +3,6 @@ + name "Test Process HISAT2_ALIGN" + script "../main.nf" + process "HISAT2_ALIGN" +- tag "modules" +- tag "modules_nfcore" +- tag "hisat2" +- tag "hisat2/align" +- tag "hisat2/build" +- tag "hisat2/extractsplicesites" + + test("Single-End") { + + +--- modules/nf-core/hisat2/align/tests/tags.yml ++++ /dev/null +@@ -1,4 +0,0 @@ +-hisat2/align: +- - modules/nf-core/hisat2/align/** +- - modules/nf-core/hisat2/build/** +- - modules/nf-core/hisat2/extractsplicesites/** + +************************************************************ diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index f45f9bccb..464a28e2b 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -34,7 +34,7 @@ process HISAT2_ALIGN { ss = "$splicesites" ? "--known-splicesite-infile $splicesites" : '' def seq_center = params.seq_center ? "--rg-id ${prefix} --rg SM:$prefix --rg CN:${params.seq_center.replaceAll('\\s','_')}" : "--rg-id ${prefix} --rg SM:$prefix" if (meta.single_end) { - def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' + def unaligned = params.save_unaligned || params.contaminant_screening ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' """ INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'` hisat2 \\ @@ -56,7 +56,7 @@ process HISAT2_ALIGN { END_VERSIONS """ } else { - def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' + def unaligned = params.save_unaligned || params.contaminant_screening ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' """ INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'` hisat2 \\ @@ -91,7 +91,8 @@ process HISAT2_ALIGN { stub: def prefix = task.ext.prefix ?: "${meta.id}" - def unaligned = params.save_unaligned ? "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz \n echo '' | gzip > ${prefix}.unmapped_2.fastq.gz" : '' + def unaligned = params.save_unaligned || params.contaminant_screening ? "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz \n echo '' | gzip > ${prefix}.unmapped_2.fastq.gz" : '' + def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ ${unaligned} diff --git a/modules/nf-core/kraken2/kraken2/environment.yml b/modules/nf-core/kraken2/kraken2/environment.yml new file mode 100644 index 000000000..0c067feeb --- /dev/null +++ b/modules/nf-core/kraken2/kraken2/environment.yml @@ -0,0 +1,9 @@ +name: kraken2_kraken2 +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::kraken2=2.1.3" + - "coreutils=9.4" + - "pigz=2.8" diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf new file mode 100644 index 000000000..364a6fe24 --- /dev/null +++ b/modules/nf-core/kraken2/kraken2/main.nf @@ -0,0 +1,85 @@ +process KRAKEN2_KRAKEN2 { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-8706a1dd73c6cc426e12dd4dd33a5e917b3989ae:c8cbdc8ff4101e6745f8ede6eb5261ef98bdaff4-0' : + 'biocontainers/mulled-v2-8706a1dd73c6cc426e12dd4dd33a5e917b3989ae:c8cbdc8ff4101e6745f8ede6eb5261ef98bdaff4-0' }" + + input: + tuple val(meta), path(reads) + path db + val save_output_fastqs + val save_reads_assignment + + output: + tuple val(meta), path('*.classified{.,_}*') , optional:true, emit: classified_reads_fastq + tuple val(meta), path('*.unclassified{.,_}*') , optional:true, emit: unclassified_reads_fastq + tuple val(meta), path('*classifiedreads.txt') , optional:true, emit: classified_reads_assignment + tuple val(meta), path('*report.txt') , emit: report + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def paired = meta.single_end ? "" : "--paired" + def classified = meta.single_end ? "${prefix}.classified.fastq" : "${prefix}.classified#.fastq" + def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq" + def classified_option = save_output_fastqs ? "--classified-out ${classified}" : "" + def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : "" + def readclassification_option = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : "--output /dev/null" + def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : "" + + """ + kraken2 \\ + --db $db \\ + --threads $task.cpus \\ + --report ${prefix}.kraken2.report.txt \\ + --gzip-compressed \\ + $unclassified_option \\ + $classified_option \\ + $readclassification_option \\ + $paired \\ + $args \\ + $reads + + $compress_reads_command + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//') + pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def paired = meta.single_end ? "" : "--paired" + def classified = meta.single_end ? "${prefix}.classified.fastq.gz" : "${prefix}.classified_1.fastq.gz ${prefix}.classified_2.fastq.gz" + def unclassified = meta.single_end ? "${prefix}.unclassified.fastq.gz" : "${prefix}.unclassified_1.fastq.gz ${prefix}.unclassified_2.fastq.gz" + def readclassification_option = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : "--output /dev/null" + def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : "" + + """ + touch ${prefix}.kraken2.report.txt + if [ "$save_output_fastqs" == "true" ]; then + touch $classified + touch $unclassified + fi + if [ "$save_reads_assignment" == "true" ]; then + touch ${prefix}.kraken2.classifiedreads.txt + fi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//') + pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) + END_VERSIONS + """ + +} diff --git a/modules/nf-core/kraken2/kraken2/meta.yml b/modules/nf-core/kraken2/kraken2/meta.yml new file mode 100644 index 000000000..7909ffe7e --- /dev/null +++ b/modules/nf-core/kraken2/kraken2/meta.yml @@ -0,0 +1,78 @@ +name: kraken2_kraken2 +description: Classifies metagenomic sequence data +keywords: + - classify + - metagenomics + - fastq + - db +tools: + - kraken2: + description: | + Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to sequence reads + homepage: https://ccb.jhu.edu/software/kraken2/ + documentation: https://github.com/DerrickWood/kraken2/wiki/Manual + doi: 10.1186/s13059-019-1891-0 + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - db: + type: directory + description: Kraken2 database + - save_output_fastqs: + type: string + description: | + If true, optional commands are added to save classified and unclassified reads + as fastq files + - save_reads_assignment: + type: string + description: | + If true, an optional command is added to save a file reporting the taxonomic + classification of each input read +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - classified_reads_fastq: + type: file + description: | + Reads classified as belonging to any of the taxa + on the Kraken2 database. + pattern: "*{fastq.gz}" + - unclassified_reads_fastq: + type: file + description: | + Reads not classified to any of the taxa + on the Kraken2 database. + pattern: "*{fastq.gz}" + - classified_reads_assignment: + type: file + description: | + Kraken2 output file indicating the taxonomic assignment of + each input read + - report: + type: file + description: | + Kraken2 report containing stats about classified + and not classifed reads. + pattern: "*.{report.txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@joseespinosa" + - "@drpatelh" +maintainers: + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/kraken2/kraken2/nextflow.config b/modules/nf-core/kraken2/kraken2/nextflow.config new file mode 100644 index 000000000..7289bd9a1 --- /dev/null +++ b/modules/nf-core/kraken2/kraken2/nextflow.config @@ -0,0 +1,15 @@ +if (!params.skip_alignment && !params.skip_qc) { + if (params.contaminant_screening in ['kraken2', 'kraken2_bracken']) { + process { + withName: 'KRAKEN2' { + // See https://doi.org/10.1080/19490976.2024.2323235 for the confidence level + // and https://doi.org/10.1038/s41596-022-00738-y for the minimum-hit-groups + ext.args = "--confidence 0.05 --minimum-hit-groups 3" + publishDir = [ + path: { "${params.outdir}/${params.aligner}/contaminants/kraken2/kraken_reports" }, + mode: params.publish_dir_mode + ] + } + } + } +} \ No newline at end of file diff --git a/modules/nf-core/kraken2/kraken2/tests/main.nf.test b/modules/nf-core/kraken2/kraken2/tests/main.nf.test new file mode 100644 index 000000000..c0843df29 --- /dev/null +++ b/modules/nf-core/kraken2/kraken2/tests/main.nf.test @@ -0,0 +1,143 @@ +nextflow_process { + name "Test Process KRAKEN2_KRAKEN2" + script "../main.nf" + process "KRAKEN2_KRAKEN2" + tag "modules" + tag "modules_nfcore" + tag "untar" + tag "kraken2" + tag "kraken2/kraken2" + + setup { + run("UNTAR") { + script "modules/nf-core/untar/main.nf" + process { + """ + input[0] = Channel.of([ + [], + file( + params.modules_testdata_base_path + "genomics/sarscov2/genome/db/kraken2.tar.gz", + checkIfExists: true + ) + ]) + """ + } + } + } + + test("sarscov2 illumina single end [fastq]") { + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + [ file( + params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", + checkIfExists: true + )] + ] + input[1] = UNTAR.out.untar.map{ it[1] } + input[2] = true + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.report, + process.out.versions, + ).match() + }, + { assert process.out.classified_reads_fastq.get(0).get(1) ==~ ".*/test.classified.fastq.gz" }, + { assert process.out.unclassified_reads_fastq.get(0).get(1) ==~ ".*/test.unclassified.fastq.gz" }, + ) + } + } + + test("sarscov2 illumina paired end [fastq]") { + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file( + params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", + checkIfExists: true + ), + file( + params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", + checkIfExists: true + ) + + ] + ] + input[1] = UNTAR.out.untar.map{ it[1] } + input[2] = true + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.report, + process.out.versions, + ).match() + }, + { assert process.out.classified_reads_fastq.get(0).get(1).get(0) + ==~ ".*/test.classified_1.fastq.gz" }, + { assert process.out.classified_reads_fastq.get(0).get(1).get(1) + ==~ ".*/test.classified_2.fastq.gz" }, + { assert process.out.unclassified_reads_fastq.get(0).get(1).get(0) + ==~ ".*/test.unclassified_1.fastq.gz" }, + { assert process.out.unclassified_reads_fastq.get(0).get(1).get(1) + ==~ ".*/test.unclassified_2.fastq.gz" }, + ) + } + } + + test("sarscov2 illumina single end [fastq] + save_reads_assignment") { + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + [ file( + params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", + checkIfExists: true + )] + ] + input[1] = UNTAR.out.untar.map{ it[1] } + input[2] = false + input[3] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.report, + process.out.classified_reads_assignment, + process.out.versions, + ).match() + }, + ) + } + } +} diff --git a/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap b/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap new file mode 100644 index 000000000..b432f878f --- /dev/null +++ b/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap @@ -0,0 +1,74 @@ +{ + "sarscov2 illumina single end [fastq]": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e" + ] + ], + [ + "versions.yml:md5,79adf2ca1cfc625cb77e391b27142c43" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-04T18:47:03.745692" + }, + "sarscov2 illumina paired end [fastq]": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e" + ] + ], + [ + "versions.yml:md5,79adf2ca1cfc625cb77e391b27142c43" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-04T18:47:13.75649" + }, + "sarscov2 illumina single end [fastq] + save_reads_assignment": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.kraken2.classifiedreads.txt:md5,e7a90531f0d8d777316515c36fe4cae0" + ] + ], + [ + "versions.yml:md5,79adf2ca1cfc625cb77e391b27142c43" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-04T18:47:22.459465" + } +} \ No newline at end of file diff --git a/modules/nf-core/kraken2/kraken2/tests/tags.yml b/modules/nf-core/kraken2/kraken2/tests/tags.yml new file mode 100644 index 000000000..9ebfd7ab6 --- /dev/null +++ b/modules/nf-core/kraken2/kraken2/tests/tags.yml @@ -0,0 +1,3 @@ +kraken2/kraken2: + - modules/nf-core/kraken2/kraken2/** + - modules/nf-core/untar/** diff --git a/nextflow.config b/nextflow.config index d5e00c6f4..94481109e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -89,6 +89,11 @@ params { skip_preseq = true skip_dupradar = false skip_qualimap = false + contaminant_screening = null + kraken_db = null + save_kraken_assignments = false + save_kraken_unassigned = false + bracken_precision = "S" skip_rseqc = false skip_biotype_qc = false skip_deseq2_qc = false diff --git a/nextflow_schema.json b/nextflow_schema.json index d89b6398e..e7cd6d468 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -518,6 +518,18 @@ "fa_icon": "fas fa-save", "description": "Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.", "help_text": "This may either be in the form of FastQ or BAM files depending on the options available for that particular tool." + }, + "save_kraken_assignments": { + "type": "boolean", + "fa_icon": "fas fa-save", + "description": "Save read-by-read assignments from Kraken2.", + "help_text": "`--kraken_db` parameter must be provided." + }, + "save_kraken_unassigned": { + "type": "boolean", + "fa_icon": "fas fa-save", + "description": "Save reads that were not given assignment from Kraken2.", + "help_text": "`--kraken_db` parameter must be provided." } } }, @@ -539,6 +551,26 @@ "default": "bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication", "fa_icon": "fas fa-chart-pie", "description": "Specify the RSeQC modules to run." + }, + "contaminant_screening": { + "type": "string", + "description": "Tool to use for detecting contaminants in unaligned reads - available options are 'kraken2' and 'kraken2_bracken'", + "fa_icon": "fas fa-virus-slash", + "enum": ["kraken2", "kraken2_bracken"] + }, + "kraken_db": { + "type": "string", + "description": "Database when using Kraken2/Bracken for contaminant screening.", + "help_text": "See the usage tab for more information", + "fa_icon": "fas fa-fish" + }, + "bracken_precision": { + "type": "string", + "default": "S", + "fa_icon": "fas fa-tree", + "description": "Taxonomic level for Bracken abundance estimations.", + "help_text": "First letter of Domain / Phylum / Class / Order / Family / Genus / Species", + "enum": ["D", "P", "C", "O", "F", "G", "S"] } } }, diff --git a/subworkflows/local/align_star/nextflow.config b/subworkflows/local/align_star/nextflow.config index 119eb6e4a..511ff6e63 100644 --- a/subworkflows/local/align_star/nextflow.config +++ b/subworkflows/local/align_star/nextflow.config @@ -22,7 +22,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') { --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend --outSAMstrandField intronMotif - ${params.save_unaligned ? '--outReadsUnmapped Fastx' : ''} + ${params.save_unaligned || params.contaminant_screening ? '--outReadsUnmapped Fastx' : ''} """.trim()) // Consolidate the extra arguments diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf index b2b890479..5d55ce0a8 100644 --- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf @@ -256,6 +256,29 @@ def validateInputParameters() { } } + //General checks for if contaminant screening is used + if (params.contaminant_screening) { + if (params.aligner == 'star_rsem') { + error("Contaminant screeneing cannot be done with --aligner star_rsem since unaligned reads are not saved. Please use --aligner star_salmon or --aligner hisat2.") + } + } + + // Check that Kraken/Bracken database provided if using kraken2/bracken + if (params.contaminant_screening in ['kraken2', 'kraken2_bracken']) { + if (!params.kraken_db) { + error("Contaminant screening set to kraken2 but not database is provided. Please provide a database with the --kraken_db option.") + } + //Check that Kraken/Bracken parameters are not provided when Kraken2 is not being used + } else { + if (!params.bracken_precision.equals('S')) { + brackenPrecisionWithoutKrakenDBWarn() + } + + if (params.save_kraken_assignments || params.save_kraken_unassigned || params.kraken_db) { + krakenArgumentsWithoutKrakenDBWarn() + } + } + // Check which RSeQC modules we are running def valid_rseqc_modules = ['bam_stat', 'inner_distance', 'infer_experiment', 'junction_annotation', 'junction_saturation', 'read_distribution', 'read_duplication', 'tin'] def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').collect{ it.trim().toLowerCase() } : [] @@ -471,6 +494,26 @@ def additionaFastaIndexWarn(index) { "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" } +// +// Print a warning if --save_kraken_assignments or --save_kraken_unassigned is provided without --kraken_db +// +def krakenArgumentsWithoutKrakenDBWarn() { + log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " 'Kraken2 related arguments have been provided without setting contaminant\n" + + " screening to Kraken2. Kraken2 is not being run so these will not be used.\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" +} + +/// +/// Print a warning if --bracken-precision is provided without --kraken_db +/// +def brackenPrecisionWithoutKrakenDBWarn() { + log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " '--bracken-precision' parameter has been provided without Kraken2 contaminant screening.\n" + + " Bracken will not run so precision will not be set.\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" +} + // // Function to generate an error if contigs in genome fasta file > 512 Mbp // diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml index ff154e1cb..63fad09f1 100644 --- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml +++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml @@ -93,6 +93,8 @@ run_modules: - preseq - rseqc - qualimap + - kraken + - bracken # Order of modules @@ -156,6 +158,12 @@ sp: samtools/idxstats: fn: "*.idxstats*" + kraken: + fn: "*report.txt" + + bracken: + fn: "*.kraken2.report_bracken.txt" + rseqc/bam_stat: fn: "*.bam_stat.txt" rseqc/gene_body_coverage: diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index 2ee8384f4..8a85cf845 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -33,13 +33,15 @@ include { methodsDescriptionText } from '../../subworkflows/local/utils_ // // MODULE: Installed directly from nf-core/modules // -include { DUPRADAR } from '../../modules/nf-core/dupradar' -include { SAMTOOLS_SORT } from '../../modules/nf-core/samtools/sort' -include { PRESEQ_LCEXTRAP } from '../../modules/nf-core/preseq/lcextrap' -include { QUALIMAP_RNASEQ } from '../../modules/nf-core/qualimap/rnaseq' -include { STRINGTIE_STRINGTIE } from '../../modules/nf-core/stringtie/stringtie' -include { SUBREAD_FEATURECOUNTS } from '../../modules/nf-core/subread/featurecounts' -include { MULTIQC } from '../../modules/nf-core/multiqc' +include { DUPRADAR } from '../../modules/nf-core/dupradar' +include { SAMTOOLS_SORT } from '../../modules/nf-core/samtools/sort' +include { PRESEQ_LCEXTRAP } from '../../modules/nf-core/preseq/lcextrap' +include { QUALIMAP_RNASEQ } from '../../modules/nf-core/qualimap/rnaseq' +include { STRINGTIE_STRINGTIE } from '../../modules/nf-core/stringtie/stringtie' +include { SUBREAD_FEATURECOUNTS } from '../../modules/nf-core/subread/featurecounts' +include { KRAKEN2_KRAKEN2 as KRAKEN2 } from '../../modules/nf-core/kraken2/kraken2/main' +include { BRACKEN_BRACKEN as BRACKEN } from '../../modules/nf-core/bracken/bracken/main' +include { MULTIQC } from '../../modules/nf-core/multiqc' include { UMITOOLS_PREPAREFORRSEM as UMITOOLS_PREPAREFORSALMON } from '../../modules/nf-core/umitools/prepareforrsem' include { BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_FW } from '../../modules/nf-core/bedtools/genomecov' include { BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_REV } from '../../modules/nf-core/bedtools/genomecov' @@ -171,9 +173,10 @@ workflow RNASEQ { // // SUBWORKFLOW: Alignment with STAR and gene/transcript quantification with Salmon // - ch_genome_bam = Channel.empty() - ch_genome_bam_index = Channel.empty() - ch_star_log = Channel.empty() + ch_genome_bam = Channel.empty() + ch_genome_bam_index = Channel.empty() + ch_star_log = Channel.empty() + ch_unaligned_sequences = Channel.empty() if (!params.skip_alignment && params.aligner == 'star_salmon') { // Check if an AWS iGenome has been provided to use the appropriate version of STAR def is_aws_igenome = false @@ -193,10 +196,11 @@ workflow RNASEQ { is_aws_igenome, ch_fasta.map { [ [:], it ] } ) - ch_genome_bam = ALIGN_STAR.out.bam - ch_genome_bam_index = ALIGN_STAR.out.bai - ch_transcriptome_bam = ALIGN_STAR.out.bam_transcript - ch_star_log = ALIGN_STAR.out.log_final + ch_genome_bam = ALIGN_STAR.out.bam + ch_genome_bam_index = ALIGN_STAR.out.bai + ch_transcriptome_bam = ALIGN_STAR.out.bam_transcript + ch_star_log = ALIGN_STAR.out.log_final + ch_unaligned_sequences = ALIGN_STAR.out.fastq ch_multiqc_files = ch_multiqc_files.mix(ALIGN_STAR.out.stats.collect{it[1]}) ch_multiqc_files = ch_multiqc_files.mix(ALIGN_STAR.out.flagstat.collect{it[1]}) ch_multiqc_files = ch_multiqc_files.mix(ALIGN_STAR.out.idxstats.collect{it[1]}) @@ -350,8 +354,9 @@ workflow RNASEQ { ch_splicesites.map { [ [:], it ] }, ch_fasta.map { [ [:], it ] } ) - ch_genome_bam = FASTQ_ALIGN_HISAT2.out.bam - ch_genome_bam_index = FASTQ_ALIGN_HISAT2.out.bai + ch_genome_bam = FASTQ_ALIGN_HISAT2.out.bam + ch_genome_bam_index = FASTQ_ALIGN_HISAT2.out.bai + ch_unaligned_sequences = FASTQ_ALIGN_HISAT2.out.fastq ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_HISAT2.out.stats.collect{it[1]}) ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_HISAT2.out.flagstat.collect{it[1]}) ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_HISAT2.out.idxstats.collect{it[1]}) @@ -647,6 +652,28 @@ workflow RNASEQ { ch_multiqc_files = ch_multiqc_files.mix(ch_fail_strand_multiqc.collectFile(name: 'fail_strand_check_mqc.tsv')) } + + if (params.contaminant_screening in ['kraken2', 'kraken2_bracken'] ) { + KRAKEN2 ( + ch_unaligned_sequences, + params.kraken_db, + params.save_kraken_assignments, + params.save_kraken_unassigned + ) + ch_kraken_reports = KRAKEN2.out.report + ch_versions = ch_versions.mix(KRAKEN2.out.versions) + + if (params.contaminant_screening == 'kraken2') { + ch_multiqc_files = ch_multiqc_files.mix(KRAKEN2.out.report.collect{it[1]}) + } else if (params.contaminant_screening == 'kraken2_bracken') { + BRACKEN ( + ch_kraken_reports, + params.kraken_db + ) + ch_versions = ch_versions.mix(BRACKEN.out.versions) + ch_multiqc_files = ch_multiqc_files.mix(BRACKEN.out.txt.collect{it[1]}) + } + } } // diff --git a/workflows/rnaseq/nextflow.config b/workflows/rnaseq/nextflow.config index c7eeac733..9cbf0cd30 100644 --- a/workflows/rnaseq/nextflow.config +++ b/workflows/rnaseq/nextflow.config @@ -8,6 +8,8 @@ includeConfig "../../modules/nf-core/qualimap/rnaseq/nextflow.config" includeConfig "../../modules/nf-core/sortmerna/nextflow.config" includeConfig "../../modules/nf-core/stringtie/stringtie/nextflow.config" includeConfig "../../modules/nf-core/subread/featurecounts/nextflow.config" +includeConfig "../../modules/nf-core/kraken2/kraken2/nextflow.config" +includeConfig "../../modules/nf-core/bracken/bracken/nextflow.config" includeConfig "../../subworkflows/local/align_star/nextflow.config" includeConfig "../../subworkflows/local/quantify_rsem/nextflow.config" includeConfig "../../subworkflows/nf-core/quantify_pseudo_alignment/nextflow.config" From 41bcd9c431f6c64387169ccb059c0c0a3dfbd152 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Thu, 19 Sep 2024 11:51:03 -0400 Subject: [PATCH 071/100] Update hisat2 patch --- modules.json | 286 +++++++++++++----- .../nf-core/hisat2/align/hisat2-align.diff | 9 +- 2 files changed, 223 insertions(+), 72 deletions(-) diff --git a/modules.json b/modules.json index 4c9ba76f1..82e0e34be 100644 --- a/modules.json +++ b/modules.json @@ -8,189 +8,272 @@ "bbmap/bbsplit": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] + "installed_by": [ + "fastq_qc_trim_filter_setstrandedness", + "modules" + ] }, "bedtools/genomecov": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bracken/bracken": { "branch": "master", "git_sha": "c214fad97b328eb6d6233f779be9ba44814a9136", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/fastq": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] + "installed_by": [ + "fastq_qc_trim_filter_setstrandedness", + "modules" + ] }, "custom/catadditionalfasta": { "branch": "master", "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/getchromsizes": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/tx2gene": { "branch": "master", "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", - "installed_by": ["modules", "quantify_pseudo_alignment"] + "installed_by": [ + "modules", + "quantify_pseudo_alignment" + ] }, "dupradar": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "fastp": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["fastq_fastqc_umitools_fastp", "modules"] + "installed_by": [ + "fastq_fastqc_umitools_fastp", + "modules" + ] }, "fastqc": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"] + "installed_by": [ + "fastq_fastqc_umitools_fastp", + "fastq_fastqc_umitools_trimgalore" + ] }, "fq/subsample": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["fastq_subsample_fq_salmon", "modules"] + "installed_by": [ + "fastq_subsample_fq_salmon", + "modules" + ] }, "gffread": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gunzip": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "hisat2/align": { "branch": "master", "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", - "installed_by": ["fastq_align_hisat2"], + "installed_by": [ + "fastq_align_hisat2" + ], "patch": "modules/nf-core/hisat2/align/hisat2-align.diff" }, "hisat2/build": { "branch": "master", "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "hisat2/extractsplicesites": { "branch": "master", "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "kallisto/index": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "kallisto/quant": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules", "quantify_pseudo_alignment"] + "installed_by": [ + "modules", + "quantify_pseudo_alignment" + ] }, "kraken2/kraken2": { "branch": "master", "git_sha": "a13d5d945742a60bbef6e5c177e81cda540f75dc", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "picard/markduplicates": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["bam_markduplicates_picard"], + "installed_by": [ + "bam_markduplicates_picard" + ], "patch": "modules/nf-core/picard/markduplicates/picard-markduplicates.diff" }, "preseq/lcextrap": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "qualimap/rnaseq": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rsem/calculateexpression": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rsem/preparereference": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rseqc/bamstat": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["bam_rseqc"] + "installed_by": [ + "bam_rseqc" + ] }, "rseqc/inferexperiment": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["bam_rseqc"] + "installed_by": [ + "bam_rseqc" + ] }, "rseqc/innerdistance": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["bam_rseqc"] + "installed_by": [ + "bam_rseqc" + ] }, "rseqc/junctionannotation": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["bam_rseqc"] + "installed_by": [ + "bam_rseqc" + ] }, "rseqc/junctionsaturation": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["bam_rseqc"] + "installed_by": [ + "bam_rseqc" + ] }, "rseqc/readdistribution": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["bam_rseqc"] + "installed_by": [ + "bam_rseqc" + ] }, "rseqc/readduplication": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["bam_rseqc"] + "installed_by": [ + "bam_rseqc" + ] }, "rseqc/tin": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["bam_rseqc"] + "installed_by": [ + "bam_rseqc" + ] }, "salmon/index": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["fastq_subsample_fq_salmon"] + "installed_by": [ + "fastq_subsample_fq_salmon" + ] }, "salmon/quant": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["fastq_subsample_fq_salmon", "modules", "quantify_pseudo_alignment"] + "installed_by": [ + "fastq_subsample_fq_salmon", + "modules", + "quantify_pseudo_alignment" + ] }, "samtools/flagstat": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["bam_stats_samtools"] + "installed_by": [ + "bam_stats_samtools" + ] }, "samtools/idxstats": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["bam_stats_samtools"] + "installed_by": [ + "bam_stats_samtools" + ] }, "samtools/index": { "branch": "master", @@ -204,82 +287,118 @@ "samtools/sort": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["bam_sort_stats_samtools"] + "installed_by": [ + "bam_sort_stats_samtools" + ] }, "samtools/stats": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["bam_stats_samtools"] + "installed_by": [ + "bam_stats_samtools" + ] }, "sortmerna": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] + "installed_by": [ + "fastq_qc_trim_filter_setstrandedness", + "modules" + ] }, "star/align": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "star/genomegenerate": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "stringtie/stringtie": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "subread/featurecounts": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "summarizedexperiment/summarizedexperiment": { "branch": "master", "git_sha": "625fbbc0531fb1717349c7f1b1c677a3b8619767", - "installed_by": ["modules", "quantify_pseudo_alignment"] + "installed_by": [ + "modules", + "quantify_pseudo_alignment" + ] }, "trimgalore": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["fastq_fastqc_umitools_trimgalore"] + "installed_by": [ + "fastq_fastqc_umitools_trimgalore" + ] }, "tximeta/tximport": { "branch": "master", "git_sha": "625fbbc0531fb1717349c7f1b1c677a3b8619767", - "installed_by": ["modules", "quantify_pseudo_alignment"] + "installed_by": [ + "modules", + "quantify_pseudo_alignment" + ] }, "ucsc/bedclip": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"] + "installed_by": [ + "bedgraph_bedclip_bedgraphtobigwig" + ] }, "ucsc/bedgraphtobigwig": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"] + "installed_by": [ + "bedgraph_bedclip_bedgraphtobigwig" + ] }, "umitools/dedup": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["bam_dedup_stats_samtools_umitools"] + "installed_by": [ + "bam_dedup_stats_samtools_umitools" + ] }, "umitools/extract": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"] + "installed_by": [ + "fastq_fastqc_umitools_fastp", + "fastq_fastqc_umitools_trimgalore" + ] }, "umitools/prepareforrsem": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -288,22 +407,30 @@ "bam_dedup_stats_samtools_umitools": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "bam_markduplicates_picard": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "bam_rseqc": { "branch": "master", "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "bam_sort_stats_samtools": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": ["fastq_align_hisat2"] + "installed_by": [ + "fastq_align_hisat2" + ] }, "bam_stats_samtools": { "branch": "master", @@ -317,55 +444,78 @@ "bedgraph_bedclip_bedgraphtobigwig": { "branch": "master", "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "fastq_align_hisat2": { "branch": "master", "git_sha": "c789476080a150f87066ca3ed42a622339a26c0b", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "fastq_fastqc_umitools_fastp": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] + "installed_by": [ + "fastq_qc_trim_filter_setstrandedness", + "subworkflows" + ] }, "fastq_fastqc_umitools_trimgalore": { "branch": "master", "git_sha": "b49b8992e5271ce427f3a7cdb29628fc58400eb5", - "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] + "installed_by": [ + "fastq_qc_trim_filter_setstrandedness", + "subworkflows" + ] }, "fastq_qc_trim_filter_setstrandedness": { "branch": "master", "git_sha": "ee3b8b84da02320fff5f3f2dc1d6f9b72d7cd5af", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "fastq_subsample_fq_salmon": { "branch": "master", "git_sha": "fbe341e9af0bb98533757f536b26d38507d31724", - "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] + "installed_by": [ + "fastq_qc_trim_filter_setstrandedness", + "subworkflows" + ] }, "quantify_pseudo_alignment": { "branch": "master", "git_sha": "fbe341e9af0bb98533757f536b26d38507d31724", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/hisat2/align/hisat2-align.diff b/modules/nf-core/hisat2/align/hisat2-align.diff index 6086520f6..2a64e4f4f 100644 --- a/modules/nf-core/hisat2/align/hisat2-align.diff +++ b/modules/nf-core/hisat2/align/hisat2-align.diff @@ -1,7 +1,7 @@ Changes in module 'nf-core/hisat2/align' --- modules/nf-core/hisat2/align/main.nf +++ modules/nf-core/hisat2/align/main.nf -@@ -36,7 +36,7 @@ +@@ -34,7 +34,7 @@ ss = "$splicesites" ? "--known-splicesite-infile $splicesites" : '' def seq_center = params.seq_center ? "--rg-id ${prefix} --rg SM:$prefix --rg CN:${params.seq_center.replaceAll('\\s','_')}" : "--rg-id ${prefix} --rg SM:$prefix" if (meta.single_end) { @@ -10,7 +10,7 @@ Changes in module 'nf-core/hisat2/align' """ INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'` hisat2 \\ -@@ -58,7 +58,7 @@ +@@ -56,7 +56,7 @@ END_VERSIONS """ } else { @@ -19,15 +19,16 @@ Changes in module 'nf-core/hisat2/align' """ INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'` hisat2 \\ -@@ -93,7 +93,7 @@ +@@ -91,7 +91,8 @@ stub: def prefix = task.ext.prefix ?: "${meta.id}" - def unaligned = params.save_unaligned ? "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz \n echo '' | gzip > ${prefix}.unmapped_2.fastq.gz" : '' + def unaligned = params.save_unaligned || params.contaminant_screening ? "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz \n echo '' | gzip > ${prefix}.unmapped_2.fastq.gz" : '' - def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. ++ def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ ${unaligned} + --- modules/nf-core/hisat2/align/tests/main.nf.test +++ modules/nf-core/hisat2/align/tests/main.nf.test From 3e0b3e96de08e740646d20bdf08c79ebde4b2c60 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Thu, 19 Sep 2024 11:52:30 -0400 Subject: [PATCH 072/100] (Hopefully) final linting fix --- modules.json | 286 ++++++++++++--------------------------------------- 1 file changed, 68 insertions(+), 218 deletions(-) diff --git a/modules.json b/modules.json index 82e0e34be..4c9ba76f1 100644 --- a/modules.json +++ b/modules.json @@ -8,272 +8,189 @@ "bbmap/bbsplit": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_qc_trim_filter_setstrandedness", - "modules" - ] + "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] }, "bedtools/genomecov": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bracken/bracken": { "branch": "master", "git_sha": "c214fad97b328eb6d6233f779be9ba44814a9136", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_qc_trim_filter_setstrandedness", - "modules" - ] + "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] }, "custom/catadditionalfasta": { "branch": "master", "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/getchromsizes": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/tx2gene": { "branch": "master", "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", - "installed_by": [ - "modules", - "quantify_pseudo_alignment" - ] + "installed_by": ["modules", "quantify_pseudo_alignment"] }, "dupradar": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastp": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_fastqc_umitools_fastp", - "modules" - ] + "installed_by": ["fastq_fastqc_umitools_fastp", "modules"] }, "fastqc": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_fastqc_umitools_fastp", - "fastq_fastqc_umitools_trimgalore" - ] + "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"] }, "fq/subsample": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_subsample_fq_salmon", - "modules" - ] + "installed_by": ["fastq_subsample_fq_salmon", "modules"] }, "gffread": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gunzip": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "hisat2/align": { "branch": "master", "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", - "installed_by": [ - "fastq_align_hisat2" - ], + "installed_by": ["fastq_align_hisat2"], "patch": "modules/nf-core/hisat2/align/hisat2-align.diff" }, "hisat2/build": { "branch": "master", "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "hisat2/extractsplicesites": { "branch": "master", "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "kallisto/index": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "kallisto/quant": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules", - "quantify_pseudo_alignment" - ] + "installed_by": ["modules", "quantify_pseudo_alignment"] }, "kraken2/kraken2": { "branch": "master", "git_sha": "a13d5d945742a60bbef6e5c177e81cda540f75dc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "picard/markduplicates": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_markduplicates_picard" - ], + "installed_by": ["bam_markduplicates_picard"], "patch": "modules/nf-core/picard/markduplicates/picard-markduplicates.diff" }, "preseq/lcextrap": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "qualimap/rnaseq": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rsem/calculateexpression": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rsem/preparereference": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rseqc/bamstat": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_rseqc" - ] + "installed_by": ["bam_rseqc"] }, "rseqc/inferexperiment": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_rseqc" - ] + "installed_by": ["bam_rseqc"] }, "rseqc/innerdistance": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_rseqc" - ] + "installed_by": ["bam_rseqc"] }, "rseqc/junctionannotation": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_rseqc" - ] + "installed_by": ["bam_rseqc"] }, "rseqc/junctionsaturation": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_rseqc" - ] + "installed_by": ["bam_rseqc"] }, "rseqc/readdistribution": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_rseqc" - ] + "installed_by": ["bam_rseqc"] }, "rseqc/readduplication": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_rseqc" - ] + "installed_by": ["bam_rseqc"] }, "rseqc/tin": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_rseqc" - ] + "installed_by": ["bam_rseqc"] }, "salmon/index": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_subsample_fq_salmon" - ] + "installed_by": ["fastq_subsample_fq_salmon"] }, "salmon/quant": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_subsample_fq_salmon", - "modules", - "quantify_pseudo_alignment" - ] + "installed_by": ["fastq_subsample_fq_salmon", "modules", "quantify_pseudo_alignment"] }, "samtools/flagstat": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", @@ -287,118 +204,82 @@ "samtools/sort": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_sort_stats_samtools" - ] + "installed_by": ["bam_sort_stats_samtools"] }, "samtools/stats": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "sortmerna": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_qc_trim_filter_setstrandedness", - "modules" - ] + "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] }, "star/align": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "stringtie/stringtie": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "subread/featurecounts": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "summarizedexperiment/summarizedexperiment": { "branch": "master", "git_sha": "625fbbc0531fb1717349c7f1b1c677a3b8619767", - "installed_by": [ - "modules", - "quantify_pseudo_alignment" - ] + "installed_by": ["modules", "quantify_pseudo_alignment"] }, "trimgalore": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_fastqc_umitools_trimgalore" - ] + "installed_by": ["fastq_fastqc_umitools_trimgalore"] }, "tximeta/tximport": { "branch": "master", "git_sha": "625fbbc0531fb1717349c7f1b1c677a3b8619767", - "installed_by": [ - "modules", - "quantify_pseudo_alignment" - ] + "installed_by": ["modules", "quantify_pseudo_alignment"] }, "ucsc/bedclip": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bedgraph_bedclip_bedgraphtobigwig" - ] + "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"] }, "ucsc/bedgraphtobigwig": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bedgraph_bedclip_bedgraphtobigwig" - ] + "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"] }, "umitools/dedup": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_dedup_stats_samtools_umitools" - ] + "installed_by": ["bam_dedup_stats_samtools_umitools"] }, "umitools/extract": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_fastqc_umitools_fastp", - "fastq_fastqc_umitools_trimgalore" - ] + "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"] }, "umitools/prepareforrsem": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -407,30 +288,22 @@ "bam_dedup_stats_samtools_umitools": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "bam_markduplicates_picard": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "bam_rseqc": { "branch": "master", "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "bam_sort_stats_samtools": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "fastq_align_hisat2" - ] + "installed_by": ["fastq_align_hisat2"] }, "bam_stats_samtools": { "branch": "master", @@ -444,78 +317,55 @@ "bedgraph_bedclip_bedgraphtobigwig": { "branch": "master", "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "fastq_align_hisat2": { "branch": "master", "git_sha": "c789476080a150f87066ca3ed42a622339a26c0b", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "fastq_fastqc_umitools_fastp": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "fastq_qc_trim_filter_setstrandedness", - "subworkflows" - ] + "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "fastq_fastqc_umitools_trimgalore": { "branch": "master", "git_sha": "b49b8992e5271ce427f3a7cdb29628fc58400eb5", - "installed_by": [ - "fastq_qc_trim_filter_setstrandedness", - "subworkflows" - ] + "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "fastq_qc_trim_filter_setstrandedness": { "branch": "master", "git_sha": "ee3b8b84da02320fff5f3f2dc1d6f9b72d7cd5af", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "fastq_subsample_fq_salmon": { "branch": "master", "git_sha": "fbe341e9af0bb98533757f536b26d38507d31724", - "installed_by": [ - "fastq_qc_trim_filter_setstrandedness", - "subworkflows" - ] + "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "quantify_pseudo_alignment": { "branch": "master", "git_sha": "fbe341e9af0bb98533757f536b26d38507d31724", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} From 02f65ab01b6f911516ae629762b7f9a81e6e0e17 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Thu, 19 Sep 2024 12:15:03 -0400 Subject: [PATCH 073/100] Change PR number --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e9c90c34c..6558baf06 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Enhancements & fixes -- [PR #1351](https://github.com/nf-core/rnaseq/pull/1351) - Adding Kraken2/Bracken on unaligned reads as an additional quality control step to detect sample contamination +- [PR #1388](https://github.com/nf-core/rnaseq/pull/1351) - Adding Kraken2/Bracken on unaligned reads as an additional quality control step to detect sample contamination - [PR #1186](https://github.com/nf-core/rnaseq/pull/1186) - Bump pipeline version to 3.16.0dev ### Parameters From a6a3107c2e2da7131e6c69a5bed03ac77b0a7094 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 19 Sep 2024 21:21:08 +0200 Subject: [PATCH 074/100] snapshots all filenames --- tests/default.nf.test | 4 +- tests/default.nf.test.snap | 294 ++++++++++++++++++- tests/featurecounts_group_type.nf.test | 8 +- tests/featurecounts_group_type.nf.test.snap | 276 +++++++++++++++++- tests/hisat2.nf.test | 8 +- tests/hisat2.nf.test.snap | 268 +++++++++++++++++- tests/kallisto.nf.test | 8 +- tests/kallisto.nf.test.snap | 37 ++- tests/min_mapped_reads.nf.test | 8 +- tests/min_mapped_reads.nf.test.snap | 235 ++++++++++++++- tests/remove_ribo_rna.nf.test | 8 +- tests/remove_ribo_rna.nf.test.snap | 298 +++++++++++++++++++- tests/salmon.nf.test | 8 +- tests/salmon.nf.test.snap | 67 ++++- tests/skip_qc.nf.test | 8 +- tests/skip_qc.nf.test.snap | 131 ++++++++- tests/skip_trimming.nf.test | 4 +- tests/skip_trimming.nf.test.snap | 265 ++++++++++++++++- tests/star_rsem.nf.test | 8 +- tests/star_rsem.nf.test.snap | 269 +++++++++++++++++- 20 files changed, 2155 insertions(+), 57 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 48ebd1d27..6763d799f 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -24,7 +24,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -55,7 +55,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 235f7b097..e262b5263 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -49,6 +49,8 @@ [ "custom", "out", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw.html", @@ -88,7 +90,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T18:13:03.370736" + "timestamp": "2024-09-19T18:59:55.019534" }, "Params: default": { "content": [ @@ -237,6 +239,8 @@ "WT_REP2.stats.txt", "custom", "out", + "genome_gfp.fasta", + "genome_gfp.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw_1_fastqc.html", @@ -276,13 +280,41 @@ "star_salmon", "multiqc_report.html", "multiqc_report_data", + "cutadapt_filtered_reads_plot.txt", + "cutadapt_trimmed_sequences_plot_3_Counts.txt", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "fastqc-status-check-heatmap-1.txt", + "fastqc-status-check-heatmap.txt", + "fastqc_adapter_content_plot.txt", + "fastqc_overrepresented_sequences_plot-1.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot-1.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot-1.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot-1.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot-1.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot-1.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", + "multiqc_citations.txt", + "multiqc_cutadapt.txt", "multiqc_data.json", "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", + "multiqc_fastqc_fastqc_raw.txt", + "multiqc_fastqc_fastqc_trimmed.txt", + "multiqc_featurecounts_biotype_plot.txt", "multiqc_general_stats.txt", "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", @@ -297,6 +329,7 @@ "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", + "multiqc_samtools_idxstats.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", @@ -308,9 +341,16 @@ "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", "picard_deduplication.txt", + "picard_histogram.txt", + "picard_histogram_1.txt", + "picard_histogram_2.txt", + "qualimap_gene_coverage_profile_Counts.txt", + "qualimap_gene_coverage_profile_Normalised.txt", "qualimap_genomic_origin.txt", + "qualimap_rnaseq_cov_hist.txt", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", + "rseqc_infer_experiment_plot.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", @@ -326,6 +366,9 @@ "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", "star_alignment_plot.txt", @@ -405,21 +448,47 @@ "star_salmon_deseq2_pca-plot.pdf", "star_summary_table.pdf", "png", + "cutadapt_filtered_reads_plot-cnt.png", + "cutadapt_filtered_reads_plot-pct.png", + "cutadapt_trimmed_sequences_plot_3_Counts.png", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "dupradar-section-plot.png", "fail_strand_check_table.png", + "fastqc-status-check-heatmap-1.png", + "fastqc-status-check-heatmap.png", "fastqc_adapter_content_plot.png", + "fastqc_overrepresented_sequences_plot-1.png", + "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot-1.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot-1.png", "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot-1_Counts.png", + "fastqc_per_sequence_gc_content_plot-1_Percentages.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot-1.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-1-cnt.png", + "fastqc_sequence_counts_plot-1-pct.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot-1.png", + "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", + "featurecounts_biotype_plot-cnt.png", + "featurecounts_biotype_plot-pct.png", "general_stats_table.png", "picard_deduplication-cnt.png", "picard_deduplication-pct.png", + "qualimap_gene_coverage_profile_Counts.png", + "qualimap_gene_coverage_profile_Normalised.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", + "rseqc_infer_experiment_plot.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", @@ -431,11 +500,18 @@ "rseqc_junction_saturation_plot_Novel_Junctions.png", "rseqc_read_distribution_plot-cnt.png", "rseqc_read_distribution_plot-pct.png", + "rseqc_read_dups_plot.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png", "samtools-stats-dp.png", "samtools_alignment_plot-cnt.png", "samtools_alignment_plot-pct.png", @@ -522,55 +598,86 @@ "salmon", "RAP1_IAA_30M_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "deseq2_qc", + "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -594,13 +701,19 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", + "tx2gene.tsv", "star_salmon", "RAP1_IAA_30M_REP1", "RAP1_IAA_30M_REP1.markdup.sorted.bam", "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -611,8 +724,13 @@ "RAP1_UNINDUCED_REP1.markdup.sorted.bam", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -623,8 +741,13 @@ "RAP1_UNINDUCED_REP2.markdup.sorted.bam", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -635,8 +758,13 @@ "WT_REP1.markdup.sorted.bam", "WT_REP1.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -647,8 +775,13 @@ "WT_REP2.markdup.sorted.bam", "WT_REP2.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -667,6 +800,7 @@ "WT_REP2.forward.bigWig", "WT_REP2.reverse.bigWig", "deseq2_qc", + "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -686,6 +820,11 @@ "WT_REP1_duprateExpBoxplot.pdf", "WT_REP2_duprateExpBoxplot.pdf", "gene_data", + "RAP1_IAA_30M_REP1_dupMatrix.txt", + "RAP1_UNINDUCED_REP1_dupMatrix.txt", + "RAP1_UNINDUCED_REP2_dupMatrix.txt", + "WT_REP1_dupMatrix.txt", + "WT_REP2_dupMatrix.txt", "histogram", "RAP1_IAA_30M_REP1_expressionHist.pdf", "RAP1_UNINDUCED_REP1_expressionHist.pdf", @@ -693,6 +832,11 @@ "WT_REP1_expressionHist.pdf", "WT_REP2_expressionHist.pdf", "intercepts_slope", + "RAP1_IAA_30M_REP1_intercept_slope.txt", + "RAP1_UNINDUCED_REP1_intercept_slope.txt", + "RAP1_UNINDUCED_REP2_intercept_slope.txt", + "WT_REP1_intercept_slope.txt", + "WT_REP2_intercept_slope.txt", "scatter_plot", "RAP1_IAA_30M_REP1_duprateExpDens.pdf", "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", @@ -700,27 +844,47 @@ "WT_REP1_duprateExpDens.pdf", "WT_REP2_duprateExpDens.pdf", "featurecounts", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv", + "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv", + "RAP1_IAA_30M_REP1.featureCounts.txt", "RAP1_IAA_30M_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv", + "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv", + "RAP1_UNINDUCED_REP1.featureCounts.txt", "RAP1_UNINDUCED_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv", + "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv", + "RAP1_UNINDUCED_REP2.featureCounts.txt", "RAP1_UNINDUCED_REP2.featureCounts.txt.summary", + "WT_REP1.biotype_counts_mqc.tsv", + "WT_REP1.biotype_counts_rrna_mqc.tsv", + "WT_REP1.featureCounts.txt", "WT_REP1.featureCounts.txt.summary", + "WT_REP2.biotype_counts_mqc.tsv", + "WT_REP2.biotype_counts_rrna_mqc.tsv", + "WT_REP2.featureCounts.txt", "WT_REP2.featureCounts.txt.summary", "log", "RAP1_IAA_30M_REP1.Log.final.out", "RAP1_IAA_30M_REP1.Log.out", "RAP1_IAA_30M_REP1.Log.progress.out", + "RAP1_IAA_30M_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP1.Log.final.out", "RAP1_UNINDUCED_REP1.Log.out", "RAP1_UNINDUCED_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP2.Log.final.out", "RAP1_UNINDUCED_REP2.Log.out", "RAP1_UNINDUCED_REP2.Log.progress.out", + "RAP1_UNINDUCED_REP2.SJ.out.tab", "WT_REP1.Log.final.out", "WT_REP1.Log.out", "WT_REP1.Log.progress.out", + "WT_REP1.SJ.out.tab", "WT_REP2.Log.final.out", "WT_REP2.Log.out", "WT_REP2.Log.progress.out", + "WT_REP2.SJ.out.tab", "picard_metrics", "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -733,90 +897,190 @@ "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "rseqc", "bam_stat", @@ -826,6 +1090,11 @@ "WT_REP1.bam_stat.txt", "WT_REP2.bam_stat.txt", "infer_experiment", + "RAP1_IAA_30M_REP1.infer_experiment.txt", + "RAP1_UNINDUCED_REP1.infer_experiment.txt", + "RAP1_UNINDUCED_REP2.infer_experiment.txt", + "WT_REP1.infer_experiment.txt", + "WT_REP2.infer_experiment.txt", "inner_distance", "pdf", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", @@ -974,30 +1243,51 @@ "WT_REP2.sorted.bam.stats", "stringtie", "RAP1_IAA_30M_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_IAA_30M_REP1.coverage.gtf", "RAP1_IAA_30M_REP1.gene.abundance.txt", "RAP1_IAA_30M_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP1.coverage.gtf", "RAP1_UNINDUCED_REP1.gene.abundance.txt", "RAP1_UNINDUCED_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP2.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP2.coverage.gtf", "RAP1_UNINDUCED_REP2.gene.abundance.txt", "RAP1_UNINDUCED_REP2.transcripts.gtf", "WT_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "WT_REP1.coverage.gtf", "WT_REP1.gene.abundance.txt", "WT_REP1.transcripts.gtf", "WT_REP2.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "WT_REP2.coverage.gtf", "WT_REP2.gene.abundance.txt", "WT_REP2.transcripts.gtf", + "tx2gene.tsv", "trimgalore", "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", @@ -1303,6 +1593,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T10:12:58.76862" + "timestamp": "2024-09-19T18:59:10.651567" } } \ No newline at end of file diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index 3cfa81189..0323dab87 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + // All stable path name + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + // All stable path name + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index c25b46548..6b66ed182 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -49,6 +49,8 @@ [ "custom", "out", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw.html", @@ -88,7 +90,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-18T11:14:05.347975" + "timestamp": "2024-09-19T19:07:58.904122" }, "Params: --featurecounts_group_type false": { "content": [ @@ -231,6 +233,8 @@ "WT_REP2.stats.txt", "custom", "out", + "genome_gfp.fasta", + "genome_gfp.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw_1_fastqc.html", @@ -270,13 +274,40 @@ "star_salmon", "multiqc_report.html", "multiqc_report_data", + "cutadapt_filtered_reads_plot.txt", + "cutadapt_trimmed_sequences_plot_3_Counts.txt", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "fastqc-status-check-heatmap-1.txt", + "fastqc-status-check-heatmap.txt", + "fastqc_adapter_content_plot.txt", + "fastqc_overrepresented_sequences_plot-1.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot-1.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot-1.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot-1.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot-1.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot-1.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", + "multiqc_citations.txt", + "multiqc_cutadapt.txt", "multiqc_data.json", "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", + "multiqc_fastqc_fastqc_raw.txt", + "multiqc_fastqc_fastqc_trimmed.txt", "multiqc_general_stats.txt", "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", @@ -291,6 +322,7 @@ "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", + "multiqc_samtools_idxstats.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", @@ -302,9 +334,16 @@ "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", "picard_deduplication.txt", + "picard_histogram.txt", + "picard_histogram_1.txt", + "picard_histogram_2.txt", + "qualimap_gene_coverage_profile_Counts.txt", + "qualimap_gene_coverage_profile_Normalised.txt", "qualimap_genomic_origin.txt", + "qualimap_rnaseq_cov_hist.txt", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", + "rseqc_infer_experiment_plot.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", @@ -320,6 +359,9 @@ "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", "star_alignment_plot.txt", @@ -397,21 +439,45 @@ "star_salmon_deseq2_pca-plot.pdf", "star_summary_table.pdf", "png", + "cutadapt_filtered_reads_plot-cnt.png", + "cutadapt_filtered_reads_plot-pct.png", + "cutadapt_trimmed_sequences_plot_3_Counts.png", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "dupradar-section-plot.png", "fail_strand_check_table.png", + "fastqc-status-check-heatmap-1.png", + "fastqc-status-check-heatmap.png", "fastqc_adapter_content_plot.png", + "fastqc_overrepresented_sequences_plot-1.png", + "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot-1.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot-1.png", "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot-1_Counts.png", + "fastqc_per_sequence_gc_content_plot-1_Percentages.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot-1.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-1-cnt.png", + "fastqc_sequence_counts_plot-1-pct.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot-1.png", + "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", "picard_deduplication-cnt.png", "picard_deduplication-pct.png", + "qualimap_gene_coverage_profile_Counts.png", + "qualimap_gene_coverage_profile_Normalised.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", + "rseqc_infer_experiment_plot.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", @@ -423,11 +489,18 @@ "rseqc_junction_saturation_plot_Novel_Junctions.png", "rseqc_read_distribution_plot-cnt.png", "rseqc_read_distribution_plot-pct.png", + "rseqc_read_dups_plot.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png", "samtools-stats-dp.png", "samtools_alignment_plot-cnt.png", "samtools_alignment_plot-pct.png", @@ -512,55 +585,86 @@ "salmon", "RAP1_IAA_30M_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "deseq2_qc", + "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -584,13 +688,19 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", + "tx2gene.tsv", "star_salmon", "RAP1_IAA_30M_REP1", "RAP1_IAA_30M_REP1.markdup.sorted.bam", "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -601,8 +711,13 @@ "RAP1_UNINDUCED_REP1.markdup.sorted.bam", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -613,8 +728,13 @@ "RAP1_UNINDUCED_REP2.markdup.sorted.bam", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -625,8 +745,13 @@ "WT_REP1.markdup.sorted.bam", "WT_REP1.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -637,8 +762,13 @@ "WT_REP2.markdup.sorted.bam", "WT_REP2.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -657,6 +787,7 @@ "WT_REP2.forward.bigWig", "WT_REP2.reverse.bigWig", "deseq2_qc", + "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -676,6 +807,11 @@ "WT_REP1_duprateExpBoxplot.pdf", "WT_REP2_duprateExpBoxplot.pdf", "gene_data", + "RAP1_IAA_30M_REP1_dupMatrix.txt", + "RAP1_UNINDUCED_REP1_dupMatrix.txt", + "RAP1_UNINDUCED_REP2_dupMatrix.txt", + "WT_REP1_dupMatrix.txt", + "WT_REP2_dupMatrix.txt", "histogram", "RAP1_IAA_30M_REP1_expressionHist.pdf", "RAP1_UNINDUCED_REP1_expressionHist.pdf", @@ -683,6 +819,11 @@ "WT_REP1_expressionHist.pdf", "WT_REP2_expressionHist.pdf", "intercepts_slope", + "RAP1_IAA_30M_REP1_intercept_slope.txt", + "RAP1_UNINDUCED_REP1_intercept_slope.txt", + "RAP1_UNINDUCED_REP2_intercept_slope.txt", + "WT_REP1_intercept_slope.txt", + "WT_REP2_intercept_slope.txt", "scatter_plot", "RAP1_IAA_30M_REP1_duprateExpDens.pdf", "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", @@ -693,18 +834,23 @@ "RAP1_IAA_30M_REP1.Log.final.out", "RAP1_IAA_30M_REP1.Log.out", "RAP1_IAA_30M_REP1.Log.progress.out", + "RAP1_IAA_30M_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP1.Log.final.out", "RAP1_UNINDUCED_REP1.Log.out", "RAP1_UNINDUCED_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP2.Log.final.out", "RAP1_UNINDUCED_REP2.Log.out", "RAP1_UNINDUCED_REP2.Log.progress.out", + "RAP1_UNINDUCED_REP2.SJ.out.tab", "WT_REP1.Log.final.out", "WT_REP1.Log.out", "WT_REP1.Log.progress.out", + "WT_REP1.SJ.out.tab", "WT_REP2.Log.final.out", "WT_REP2.Log.out", "WT_REP2.Log.progress.out", + "WT_REP2.SJ.out.tab", "picard_metrics", "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -717,90 +863,190 @@ "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "rseqc", "bam_stat", @@ -810,6 +1056,11 @@ "WT_REP1.bam_stat.txt", "WT_REP2.bam_stat.txt", "infer_experiment", + "RAP1_IAA_30M_REP1.infer_experiment.txt", + "RAP1_UNINDUCED_REP1.infer_experiment.txt", + "RAP1_UNINDUCED_REP2.infer_experiment.txt", + "WT_REP1.infer_experiment.txt", + "WT_REP2.infer_experiment.txt", "inner_distance", "pdf", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", @@ -958,30 +1209,51 @@ "WT_REP2.sorted.bam.stats", "stringtie", "RAP1_IAA_30M_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_IAA_30M_REP1.coverage.gtf", "RAP1_IAA_30M_REP1.gene.abundance.txt", "RAP1_IAA_30M_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP1.coverage.gtf", "RAP1_UNINDUCED_REP1.gene.abundance.txt", "RAP1_UNINDUCED_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP2.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP2.coverage.gtf", "RAP1_UNINDUCED_REP2.gene.abundance.txt", "RAP1_UNINDUCED_REP2.transcripts.gtf", "WT_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "WT_REP1.coverage.gtf", "WT_REP1.gene.abundance.txt", "WT_REP1.transcripts.gtf", "WT_REP2.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "WT_REP2.coverage.gtf", "WT_REP2.gene.abundance.txt", "WT_REP2.transcripts.gtf", + "tx2gene.tsv", "trimgalore", "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", @@ -1269,6 +1541,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T10:21:06.207795" + "timestamp": "2024-09-19T19:07:14.922532" } } \ No newline at end of file diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 76d2c8ea7..9cbb2e1aa 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + // All stable path name + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + // All stable path name + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 9f39f47eb..e22c96e5c 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -50,6 +50,8 @@ [ "custom", "out", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw.html", @@ -89,7 +91,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T18:45:38.656164" + "timestamp": "2024-09-19T19:13:54.347768" }, "Params: --aligner hisat2": { "content": [ @@ -234,6 +236,8 @@ "WT_REP2.stats.txt", "custom", "out", + "genome_gfp.fasta", + "genome_gfp.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw_1_fastqc.html", @@ -299,6 +303,11 @@ "WT_REP1_duprateExpBoxplot.pdf", "WT_REP2_duprateExpBoxplot.pdf", "gene_data", + "RAP1_IAA_30M_REP1_dupMatrix.txt", + "RAP1_UNINDUCED_REP1_dupMatrix.txt", + "RAP1_UNINDUCED_REP2_dupMatrix.txt", + "WT_REP1_dupMatrix.txt", + "WT_REP2_dupMatrix.txt", "histogram", "RAP1_IAA_30M_REP1_expressionHist.pdf", "RAP1_UNINDUCED_REP1_expressionHist.pdf", @@ -306,6 +315,11 @@ "WT_REP1_expressionHist.pdf", "WT_REP2_expressionHist.pdf", "intercepts_slope", + "RAP1_IAA_30M_REP1_intercept_slope.txt", + "RAP1_UNINDUCED_REP1_intercept_slope.txt", + "RAP1_UNINDUCED_REP2_intercept_slope.txt", + "WT_REP1_intercept_slope.txt", + "WT_REP2_intercept_slope.txt", "scatter_plot", "RAP1_IAA_30M_REP1_duprateExpDens.pdf", "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", @@ -313,12 +327,32 @@ "WT_REP1_duprateExpDens.pdf", "WT_REP2_duprateExpDens.pdf", "featurecounts", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv", + "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv", + "RAP1_IAA_30M_REP1.featureCounts.txt", "RAP1_IAA_30M_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv", + "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv", + "RAP1_UNINDUCED_REP1.featureCounts.txt", "RAP1_UNINDUCED_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv", + "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv", + "RAP1_UNINDUCED_REP2.featureCounts.txt", "RAP1_UNINDUCED_REP2.featureCounts.txt.summary", + "WT_REP1.biotype_counts_mqc.tsv", + "WT_REP1.biotype_counts_rrna_mqc.tsv", + "WT_REP1.featureCounts.txt", "WT_REP1.featureCounts.txt.summary", + "WT_REP2.biotype_counts_mqc.tsv", + "WT_REP2.biotype_counts_rrna_mqc.tsv", + "WT_REP2.featureCounts.txt", "WT_REP2.featureCounts.txt.summary", "log", + "RAP1_IAA_30M_REP1.hisat2.summary.log", + "RAP1_UNINDUCED_REP1.hisat2.summary.log", + "RAP1_UNINDUCED_REP2.hisat2.summary.log", + "WT_REP1.hisat2.summary.log", + "WT_REP2.hisat2.summary.log", "picard_metrics", "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -331,90 +365,190 @@ "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "rseqc", "bam_stat", @@ -424,6 +558,11 @@ "WT_REP1.bam_stat.txt", "WT_REP2.bam_stat.txt", "infer_experiment", + "RAP1_IAA_30M_REP1.infer_experiment.txt", + "RAP1_UNINDUCED_REP1.infer_experiment.txt", + "RAP1_UNINDUCED_REP2.infer_experiment.txt", + "WT_REP1.infer_experiment.txt", + "WT_REP2.infer_experiment.txt", "inner_distance", "pdf", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", @@ -560,26 +699,46 @@ "WT_REP2.sorted.bam.stats", "stringtie", "RAP1_IAA_30M_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_IAA_30M_REP1.coverage.gtf", "RAP1_IAA_30M_REP1.gene.abundance.txt", "RAP1_IAA_30M_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP1.coverage.gtf", "RAP1_UNINDUCED_REP1.gene.abundance.txt", "RAP1_UNINDUCED_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP2.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP2.coverage.gtf", "RAP1_UNINDUCED_REP2.gene.abundance.txt", "RAP1_UNINDUCED_REP2.transcripts.gtf", "WT_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "WT_REP1.coverage.gtf", "WT_REP1.gene.abundance.txt", "WT_REP1.transcripts.gtf", "WT_REP2.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "WT_REP2.coverage.gtf", "WT_REP2.gene.abundance.txt", @@ -588,14 +747,43 @@ "hisat2", "multiqc_report.html", "multiqc_report_data", + "cutadapt_filtered_reads_plot.txt", + "cutadapt_trimmed_sequences_plot_3_Counts.txt", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "fastqc-status-check-heatmap-1.txt", + "fastqc-status-check-heatmap.txt", + "fastqc_adapter_content_plot.txt", + "fastqc_overrepresented_sequences_plot-1.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot-1.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot-1.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot-1.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot-1.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot-1.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "hisat2_pe_plot.txt", + "hisat2_se_plot.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", + "multiqc_citations.txt", + "multiqc_cutadapt.txt", "multiqc_data.json", "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", + "multiqc_fastqc_fastqc_raw.txt", + "multiqc_fastqc_fastqc_trimmed.txt", + "multiqc_featurecounts_biotype_plot.txt", "multiqc_general_stats.txt", "multiqc_hisat2.txt", "multiqc_picard_dups.txt", @@ -611,13 +799,21 @@ "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", + "multiqc_samtools_idxstats.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", "picard_deduplication.txt", + "picard_histogram.txt", + "picard_histogram_1.txt", + "picard_histogram_2.txt", + "qualimap_gene_coverage_profile_Counts.txt", + "qualimap_gene_coverage_profile_Normalised.txt", "qualimap_genomic_origin.txt", + "qualimap_rnaseq_cov_hist.txt", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", + "rseqc_infer_experiment_plot.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", @@ -633,6 +829,9 @@ "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", "multiqc_report_plots", @@ -709,15 +908,38 @@ "samtools_alignment_plot-cnt.pdf", "samtools_alignment_plot-pct.pdf", "png", + "cutadapt_filtered_reads_plot-cnt.png", + "cutadapt_filtered_reads_plot-pct.png", + "cutadapt_trimmed_sequences_plot_3_Counts.png", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "dupradar-section-plot.png", "fail_strand_check_table.png", + "fastqc-status-check-heatmap-1.png", + "fastqc-status-check-heatmap.png", "fastqc_adapter_content_plot.png", + "fastqc_overrepresented_sequences_plot-1.png", + "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot-1.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot-1.png", "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot-1_Counts.png", + "fastqc_per_sequence_gc_content_plot-1_Percentages.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot-1.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-1-cnt.png", + "fastqc_sequence_counts_plot-1-pct.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot-1.png", + "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", + "featurecounts_biotype_plot-cnt.png", + "featurecounts_biotype_plot-pct.png", "general_stats_table.png", "hisat2_pe_plot-cnt.png", "hisat2_pe_plot-pct.png", @@ -725,9 +947,12 @@ "hisat2_se_plot-pct.png", "picard_deduplication-cnt.png", "picard_deduplication-pct.png", + "qualimap_gene_coverage_profile_Counts.png", + "qualimap_gene_coverage_profile_Normalised.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", + "rseqc_infer_experiment_plot.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", @@ -739,11 +964,18 @@ "rseqc_junction_saturation_plot_Novel_Junctions.png", "rseqc_read_distribution_plot-cnt.png", "rseqc_read_distribution_plot-pct.png", + "rseqc_read_dups_plot.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png", "samtools-stats-dp.png", "samtools_alignment_plot-cnt.png", "samtools_alignment_plot-pct.png", @@ -824,55 +1056,86 @@ "salmon", "RAP1_IAA_30M_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "deseq2_qc", + "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -896,6 +1159,7 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", + "tx2gene.tsv", "trimgalore", "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", @@ -1175,6 +1439,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T10:28:23.826076" + "timestamp": "2024-09-19T19:13:07.804677" } } \ No newline at end of file diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index a232dc9c7..ee9b7c50e 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -26,8 +26,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + // All stable path name + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -60,8 +60,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + // All stable path name + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 708e58da1..1cf20c754 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -68,6 +68,8 @@ "WT_REP2.stats.txt", "custom", "out", + "genome_gfp.fasta", + "genome_gfp.gtf", "fastqc", "trim", "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", @@ -124,12 +126,29 @@ "kallisto.merged.transcript_counts.tsv", "kallisto.merged.transcript_lengths.tsv", "kallisto.merged.transcript_tpm.tsv", + "tx2gene.tsv", "multiqc", "multiqc_report.html", "multiqc_report_data", + "cutadapt_filtered_reads_plot.txt", + "cutadapt_trimmed_sequences_plot_3_Counts.txt", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table.txt", "kallisto_alignment.txt", + "multiqc_citations.txt", + "multiqc_cutadapt.txt", "multiqc_data.json", + "multiqc_fastqc_fastqc_trimmed.txt", "multiqc_general_stats.txt", "multiqc_kallisto.txt", "multiqc_software_versions.txt", @@ -156,8 +175,20 @@ "kallisto_alignment-cnt.pdf", "kallisto_alignment-pct.pdf", "png", + "cutadapt_filtered_reads_plot-cnt.png", + "cutadapt_filtered_reads_plot-pct.png", + "cutadapt_trimmed_sequences_plot_3_Counts.png", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", @@ -233,7 +264,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T10:32:38.720378" + "timestamp": "2024-09-19T19:17:00.197522" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ @@ -280,6 +311,8 @@ [ "custom", "out", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", "fastqc", "trim", "multiqc", @@ -307,6 +340,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T18:49:45.661258" + "timestamp": "2024-09-19T19:17:38.870034" } } \ No newline at end of file diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index 361315a5a..080dc70fe 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + // All stable path name + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + // All stable path name + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 38c70dccb..1323e1090 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -146,6 +146,8 @@ "WT_REP2.stats.txt", "custom", "out", + "genome_gfp.fasta", + "genome_gfp.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw_1_fastqc.html", @@ -185,13 +187,42 @@ "star_salmon", "multiqc_report.html", "multiqc_report_data", + "cutadapt_filtered_reads_plot.txt", + "cutadapt_trimmed_sequences_plot_3_Counts.txt", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "fastqc-status-check-heatmap-1.txt", + "fastqc-status-check-heatmap.txt", + "fastqc_adapter_content_plot.txt", + "fastqc_overrepresented_sequences_plot-1.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot-1.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot-1.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot-1.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot-1.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot-1.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", + "multiqc_citations.txt", + "multiqc_cutadapt.txt", "multiqc_data.json", "multiqc_dupradar-section-plot.txt", + "multiqc_fail_mapped_samples_table.txt", "multiqc_fail_strand_check_table.txt", + "multiqc_fastqc_fastqc_raw.txt", + "multiqc_fastqc_fastqc_trimmed.txt", + "multiqc_featurecounts_biotype_plot.txt", "multiqc_general_stats.txt", "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", @@ -206,6 +237,7 @@ "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", + "multiqc_samtools_idxstats.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", @@ -217,9 +249,16 @@ "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", "picard_deduplication.txt", + "picard_histogram.txt", + "picard_histogram_1.txt", + "picard_histogram_2.txt", + "qualimap_gene_coverage_profile_Counts.txt", + "qualimap_gene_coverage_profile_Normalised.txt", "qualimap_genomic_origin.txt", + "qualimap_rnaseq_cov_hist.txt", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", + "rseqc_infer_experiment_plot.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", @@ -235,6 +274,9 @@ "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", "star_alignment_plot.txt", @@ -315,22 +357,48 @@ "star_salmon_deseq2_pca-plot.pdf", "star_summary_table.pdf", "png", + "cutadapt_filtered_reads_plot-cnt.png", + "cutadapt_filtered_reads_plot-pct.png", + "cutadapt_trimmed_sequences_plot_3_Counts.png", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "dupradar-section-plot.png", "fail_mapped_samples_table.png", "fail_strand_check_table.png", + "fastqc-status-check-heatmap-1.png", + "fastqc-status-check-heatmap.png", "fastqc_adapter_content_plot.png", + "fastqc_overrepresented_sequences_plot-1.png", + "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot-1.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot-1.png", "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot-1_Counts.png", + "fastqc_per_sequence_gc_content_plot-1_Percentages.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot-1.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-1-cnt.png", + "fastqc_sequence_counts_plot-1-pct.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot-1.png", + "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", + "featurecounts_biotype_plot-cnt.png", + "featurecounts_biotype_plot-pct.png", "general_stats_table.png", "picard_deduplication-cnt.png", "picard_deduplication-pct.png", + "qualimap_gene_coverage_profile_Counts.png", + "qualimap_gene_coverage_profile_Normalised.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", + "rseqc_infer_experiment_plot.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", @@ -342,11 +410,18 @@ "rseqc_junction_saturation_plot_Novel_Junctions.png", "rseqc_read_distribution_plot-cnt.png", "rseqc_read_distribution_plot-pct.png", + "rseqc_read_dups_plot.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png", "samtools-stats-dp.png", "samtools_alignment_plot-cnt.png", "samtools_alignment_plot-pct.png", @@ -434,55 +509,86 @@ "salmon", "RAP1_IAA_30M_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "deseq2_qc", + "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -506,13 +612,19 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", + "tx2gene.tsv", "star_salmon", "RAP1_IAA_30M_REP1", "RAP1_IAA_30M_REP1.markdup.sorted.bam", "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -523,8 +635,13 @@ "RAP1_UNINDUCED_REP1.markdup.sorted.bam", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -535,8 +652,13 @@ "RAP1_UNINDUCED_REP2.markdup.sorted.bam", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -545,8 +667,13 @@ "quant.sf", "WT_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -555,8 +682,13 @@ "quant.sf", "WT_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -571,6 +703,7 @@ "RAP1_UNINDUCED_REP2.forward.bigWig", "RAP1_UNINDUCED_REP2.reverse.bigWig", "deseq2_qc", + "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -588,35 +721,55 @@ "RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf", "RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf", "gene_data", + "RAP1_IAA_30M_REP1_dupMatrix.txt", + "RAP1_UNINDUCED_REP1_dupMatrix.txt", + "RAP1_UNINDUCED_REP2_dupMatrix.txt", "histogram", "RAP1_IAA_30M_REP1_expressionHist.pdf", "RAP1_UNINDUCED_REP1_expressionHist.pdf", "RAP1_UNINDUCED_REP2_expressionHist.pdf", "intercepts_slope", + "RAP1_IAA_30M_REP1_intercept_slope.txt", + "RAP1_UNINDUCED_REP1_intercept_slope.txt", + "RAP1_UNINDUCED_REP2_intercept_slope.txt", "scatter_plot", "RAP1_IAA_30M_REP1_duprateExpDens.pdf", "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", "RAP1_UNINDUCED_REP2_duprateExpDens.pdf", "featurecounts", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv", + "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv", + "RAP1_IAA_30M_REP1.featureCounts.txt", "RAP1_IAA_30M_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv", + "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv", + "RAP1_UNINDUCED_REP1.featureCounts.txt", "RAP1_UNINDUCED_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv", + "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv", + "RAP1_UNINDUCED_REP2.featureCounts.txt", "RAP1_UNINDUCED_REP2.featureCounts.txt.summary", "log", "RAP1_IAA_30M_REP1.Log.final.out", "RAP1_IAA_30M_REP1.Log.out", "RAP1_IAA_30M_REP1.Log.progress.out", + "RAP1_IAA_30M_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP1.Log.final.out", "RAP1_UNINDUCED_REP1.Log.out", "RAP1_UNINDUCED_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP2.Log.final.out", "RAP1_UNINDUCED_REP2.Log.out", "RAP1_UNINDUCED_REP2.Log.progress.out", + "RAP1_UNINDUCED_REP2.SJ.out.tab", "WT_REP1.Log.final.out", "WT_REP1.Log.out", "WT_REP1.Log.progress.out", + "WT_REP1.SJ.out.tab", "WT_REP2.Log.final.out", "WT_REP2.Log.out", "WT_REP2.Log.progress.out", + "WT_REP2.SJ.out.tab", "picard_metrics", "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -627,54 +780,114 @@ "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "rseqc", "bam_stat", @@ -682,6 +895,9 @@ "RAP1_UNINDUCED_REP1.bam_stat.txt", "RAP1_UNINDUCED_REP2.bam_stat.txt", "infer_experiment", + "RAP1_IAA_30M_REP1.infer_experiment.txt", + "RAP1_UNINDUCED_REP1.infer_experiment.txt", + "RAP1_UNINDUCED_REP2.infer_experiment.txt", "inner_distance", "pdf", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", @@ -786,20 +1002,33 @@ "WT_REP2.sorted.bam.stats", "stringtie", "RAP1_IAA_30M_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_IAA_30M_REP1.coverage.gtf", "RAP1_IAA_30M_REP1.gene.abundance.txt", "RAP1_IAA_30M_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP1.coverage.gtf", "RAP1_UNINDUCED_REP1.gene.abundance.txt", "RAP1_UNINDUCED_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP2.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP2.coverage.gtf", "RAP1_UNINDUCED_REP2.gene.abundance.txt", "RAP1_UNINDUCED_REP2.transcripts.gtf", + "tx2gene.tsv", "trimgalore", "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", @@ -1046,7 +1275,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T10:41:32.333555" + "timestamp": "2024-09-19T19:24:21.094029" }, "Params: --min_mapped_reads 90 - stub": { "content": [ @@ -1098,6 +1327,8 @@ [ "custom", "out", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw.html", @@ -1137,6 +1368,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T18:57:25.990278" + "timestamp": "2024-09-19T19:25:05.823677" } } \ No newline at end of file diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index 8b757b1c6..1766dbdf6 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + // All stable path name + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + // All stable path name + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index d73fc190a..a80ccee83 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -1,7 +1,7 @@ { "Params: --remove_ribo_rna": { "content": [ - 205, + 207, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -152,6 +152,8 @@ "WT_REP2.stats.txt", "custom", "out", + "genome_gfp.fasta", + "genome_gfp.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw_1_fastqc.html", @@ -191,13 +193,41 @@ "star_salmon", "multiqc_report.html", "multiqc_report_data", + "cutadapt_filtered_reads_plot.txt", + "cutadapt_trimmed_sequences_plot_3_Counts.txt", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "fastqc-status-check-heatmap-1.txt", + "fastqc-status-check-heatmap.txt", + "fastqc_adapter_content_plot.txt", + "fastqc_overrepresented_sequences_plot-1.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot-1.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot-1.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot-1.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot-1.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot-1.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", + "multiqc_citations.txt", + "multiqc_cutadapt.txt", "multiqc_data.json", "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", + "multiqc_fastqc_fastqc_raw.txt", + "multiqc_fastqc_fastqc_trimmed.txt", + "multiqc_featurecounts_biotype_plot.txt", "multiqc_general_stats.txt", "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", @@ -212,6 +242,7 @@ "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", + "multiqc_samtools_idxstats.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sortmerna.txt", @@ -224,9 +255,16 @@ "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", "picard_deduplication.txt", + "picard_histogram.txt", + "picard_histogram_1.txt", + "picard_histogram_2.txt", + "qualimap_gene_coverage_profile_Counts.txt", + "qualimap_gene_coverage_profile_Normalised.txt", "qualimap_genomic_origin.txt", + "qualimap_rnaseq_cov_hist.txt", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", + "rseqc_infer_experiment_plot.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", @@ -242,6 +280,9 @@ "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", "sortmerna-detailed-plot.txt", @@ -324,21 +365,47 @@ "star_salmon_deseq2_pca-plot.pdf", "star_summary_table.pdf", "png", + "cutadapt_filtered_reads_plot-cnt.png", + "cutadapt_filtered_reads_plot-pct.png", + "cutadapt_trimmed_sequences_plot_3_Counts.png", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "dupradar-section-plot.png", "fail_strand_check_table.png", + "fastqc-status-check-heatmap-1.png", + "fastqc-status-check-heatmap.png", "fastqc_adapter_content_plot.png", + "fastqc_overrepresented_sequences_plot-1.png", + "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot-1.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot-1.png", "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot-1_Counts.png", + "fastqc_per_sequence_gc_content_plot-1_Percentages.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot-1.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-1-cnt.png", + "fastqc_sequence_counts_plot-1-pct.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot-1.png", + "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", + "featurecounts_biotype_plot-cnt.png", + "featurecounts_biotype_plot-pct.png", "general_stats_table.png", "picard_deduplication-cnt.png", "picard_deduplication-pct.png", + "qualimap_gene_coverage_profile_Counts.png", + "qualimap_gene_coverage_profile_Normalised.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", + "rseqc_infer_experiment_plot.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", @@ -350,14 +417,23 @@ "rseqc_junction_saturation_plot_Novel_Junctions.png", "rseqc_read_distribution_plot-cnt.png", "rseqc_read_distribution_plot-pct.png", + "rseqc_read_dups_plot.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png", "samtools-stats-dp.png", "samtools_alignment_plot-cnt.png", "samtools_alignment_plot-pct.png", + "sortmerna-detailed-plot-cnt.png", + "sortmerna-detailed-plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", "star_salmon_deseq2_clustering-plot.png", @@ -443,55 +519,86 @@ "salmon", "RAP1_IAA_30M_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "deseq2_qc", + "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -515,6 +622,7 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", + "tx2gene.tsv", "sortmerna", "RAP1_IAA_30M_REP1.sortmerna.log", "RAP1_UNINDUCED_REP1.sortmerna.log", @@ -526,8 +634,13 @@ "RAP1_IAA_30M_REP1.markdup.sorted.bam", "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -538,8 +651,13 @@ "RAP1_UNINDUCED_REP1.markdup.sorted.bam", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -550,8 +668,13 @@ "RAP1_UNINDUCED_REP2.markdup.sorted.bam", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -562,8 +685,13 @@ "WT_REP1.markdup.sorted.bam", "WT_REP1.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -574,8 +702,13 @@ "WT_REP2.markdup.sorted.bam", "WT_REP2.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -594,6 +727,7 @@ "WT_REP2.forward.bigWig", "WT_REP2.reverse.bigWig", "deseq2_qc", + "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -613,6 +747,11 @@ "WT_REP1_duprateExpBoxplot.pdf", "WT_REP2_duprateExpBoxplot.pdf", "gene_data", + "RAP1_IAA_30M_REP1_dupMatrix.txt", + "RAP1_UNINDUCED_REP1_dupMatrix.txt", + "RAP1_UNINDUCED_REP2_dupMatrix.txt", + "WT_REP1_dupMatrix.txt", + "WT_REP2_dupMatrix.txt", "histogram", "RAP1_IAA_30M_REP1_expressionHist.pdf", "RAP1_UNINDUCED_REP1_expressionHist.pdf", @@ -620,6 +759,11 @@ "WT_REP1_expressionHist.pdf", "WT_REP2_expressionHist.pdf", "intercepts_slope", + "RAP1_IAA_30M_REP1_intercept_slope.txt", + "RAP1_UNINDUCED_REP1_intercept_slope.txt", + "RAP1_UNINDUCED_REP2_intercept_slope.txt", + "WT_REP1_intercept_slope.txt", + "WT_REP2_intercept_slope.txt", "scatter_plot", "RAP1_IAA_30M_REP1_duprateExpDens.pdf", "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", @@ -627,27 +771,47 @@ "WT_REP1_duprateExpDens.pdf", "WT_REP2_duprateExpDens.pdf", "featurecounts", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv", + "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv", + "RAP1_IAA_30M_REP1.featureCounts.txt", "RAP1_IAA_30M_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv", + "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv", + "RAP1_UNINDUCED_REP1.featureCounts.txt", "RAP1_UNINDUCED_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv", + "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv", + "RAP1_UNINDUCED_REP2.featureCounts.txt", "RAP1_UNINDUCED_REP2.featureCounts.txt.summary", + "WT_REP1.biotype_counts_mqc.tsv", + "WT_REP1.biotype_counts_rrna_mqc.tsv", + "WT_REP1.featureCounts.txt", "WT_REP1.featureCounts.txt.summary", + "WT_REP2.biotype_counts_mqc.tsv", + "WT_REP2.biotype_counts_rrna_mqc.tsv", + "WT_REP2.featureCounts.txt", "WT_REP2.featureCounts.txt.summary", "log", "RAP1_IAA_30M_REP1.Log.final.out", "RAP1_IAA_30M_REP1.Log.out", "RAP1_IAA_30M_REP1.Log.progress.out", + "RAP1_IAA_30M_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP1.Log.final.out", "RAP1_UNINDUCED_REP1.Log.out", "RAP1_UNINDUCED_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP2.Log.final.out", "RAP1_UNINDUCED_REP2.Log.out", "RAP1_UNINDUCED_REP2.Log.progress.out", + "RAP1_UNINDUCED_REP2.SJ.out.tab", "WT_REP1.Log.final.out", "WT_REP1.Log.out", "WT_REP1.Log.progress.out", + "WT_REP1.SJ.out.tab", "WT_REP2.Log.final.out", "WT_REP2.Log.out", "WT_REP2.Log.progress.out", + "WT_REP2.SJ.out.tab", "picard_metrics", "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -660,90 +824,190 @@ "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "rseqc", "bam_stat", @@ -753,6 +1017,11 @@ "WT_REP1.bam_stat.txt", "WT_REP2.bam_stat.txt", "infer_experiment", + "RAP1_IAA_30M_REP1.infer_experiment.txt", + "RAP1_UNINDUCED_REP1.infer_experiment.txt", + "RAP1_UNINDUCED_REP2.infer_experiment.txt", + "WT_REP1.infer_experiment.txt", + "WT_REP2.infer_experiment.txt", "inner_distance", "pdf", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", @@ -901,30 +1170,51 @@ "WT_REP2.sorted.bam.stats", "stringtie", "RAP1_IAA_30M_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_IAA_30M_REP1.coverage.gtf", "RAP1_IAA_30M_REP1.gene.abundance.txt", "RAP1_IAA_30M_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP1.coverage.gtf", "RAP1_UNINDUCED_REP1.gene.abundance.txt", "RAP1_UNINDUCED_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP2.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP2.coverage.gtf", "RAP1_UNINDUCED_REP2.gene.abundance.txt", "RAP1_UNINDUCED_REP2.transcripts.gtf", "WT_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "WT_REP1.coverage.gtf", "WT_REP1.gene.abundance.txt", "WT_REP1.transcripts.gtf", "WT_REP2.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "WT_REP2.coverage.gtf", "WT_REP2.gene.abundance.txt", "WT_REP2.transcripts.gtf", + "tx2gene.tsv", "trimgalore", "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", @@ -1232,7 +1522,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T10:54:06.730344" + "timestamp": "2024-09-19T19:36:38.346296" }, "Params: --remove_ribo_rna - stub": { "content": [ @@ -1287,6 +1577,8 @@ [ "custom", "out", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw.html", @@ -1326,6 +1618,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T19:10:02.333783" + "timestamp": "2024-09-19T19:37:24.981917" } } \ No newline at end of file diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index 3d373840c..d051dddb3 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -26,8 +26,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + // All stable path name + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -60,8 +60,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + // All stable path name + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index ecd8d2e93..6ec67755a 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -62,6 +62,8 @@ "WT_REP2.stats.txt", "custom", "out", + "genome_gfp.fasta", + "genome_gfp.gtf", "fastqc", "trim", "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", @@ -83,8 +85,24 @@ "multiqc", "multiqc_report.html", "multiqc_report_data", + "cutadapt_filtered_reads_plot.txt", + "cutadapt_trimmed_sequences_plot_3_Counts.txt", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table.txt", + "multiqc_citations.txt", + "multiqc_cutadapt.txt", "multiqc_data.json", + "multiqc_fastqc_fastqc_trimmed.txt", "multiqc_general_stats.txt", "multiqc_salmon.txt", "multiqc_software_versions.txt", @@ -111,8 +129,20 @@ "general_stats_table.pdf", "salmon_plot.pdf", "png", + "cutadapt_filtered_reads_plot-cnt.png", + "cutadapt_filtered_reads_plot-pct.png", + "cutadapt_trimmed_sequences_plot_3_Counts.png", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", @@ -141,50 +171,80 @@ "salmon", "RAP1_IAA_30M_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", @@ -201,6 +261,7 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", + "tx2gene.tsv", "trimgalore", "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", @@ -279,7 +340,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T10:58:01.584391" + "timestamp": "2024-09-19T19:40:28.607731" }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ @@ -323,6 +384,8 @@ [ "custom", "out", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", "fastqc", "trim", "multiqc", @@ -350,6 +413,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T19:14:07.935482" + "timestamp": "2024-09-19T19:41:05.28637" } } \ No newline at end of file diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index 5d3d876bc..64eae6885 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + // All stable path name + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + // All stable path name + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 804c4d71c..316818792 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -46,6 +46,8 @@ [ "custom", "out", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", "fastqc", "trim", "multiqc", @@ -74,7 +76,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T19:24:13.457444" + "timestamp": "2024-09-19T19:47:43.501368" }, "Params: --skip_qc": { "content": [ @@ -179,6 +181,8 @@ "WT_REP2.stats.txt", "custom", "out", + "genome_gfp.fasta", + "genome_gfp.gtf", "fastqc", "trim", "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", @@ -201,20 +205,43 @@ "star_salmon", "multiqc_report.html", "multiqc_report_data", + "cutadapt_filtered_reads_plot.txt", + "cutadapt_trimmed_sequences_plot_3_Counts.txt", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table.txt", + "multiqc_citations.txt", + "multiqc_cutadapt.txt", "multiqc_data.json", + "multiqc_fastqc_fastqc_trimmed.txt", "multiqc_general_stats.txt", "multiqc_picard_dups.txt", "multiqc_salmon.txt", "multiqc_samtools_flagstat.txt", + "multiqc_samtools_idxstats.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", "multiqc_star.txt", "picard_deduplication.txt", + "picard_histogram.txt", + "picard_histogram_1.txt", + "picard_histogram_2.txt", "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", "star_alignment_plot.txt", @@ -256,8 +283,20 @@ "star_alignment_plot-pct.pdf", "star_summary_table.pdf", "png", + "cutadapt_filtered_reads_plot-cnt.png", + "cutadapt_filtered_reads_plot-pct.png", + "cutadapt_trimmed_sequences_plot_3_Counts.png", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", @@ -266,6 +305,12 @@ "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png", "samtools-stats-dp.png", "samtools_alignment_plot-cnt.png", "samtools_alignment_plot-pct.png", @@ -312,50 +357,80 @@ "salmon", "RAP1_IAA_30M_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", @@ -372,13 +447,19 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", + "tx2gene.tsv", "star_salmon", "RAP1_IAA_30M_REP1", "RAP1_IAA_30M_REP1.markdup.sorted.bam", "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -389,8 +470,13 @@ "RAP1_UNINDUCED_REP1.markdup.sorted.bam", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -401,8 +487,13 @@ "RAP1_UNINDUCED_REP2.markdup.sorted.bam", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -413,8 +504,13 @@ "WT_REP1.markdup.sorted.bam", "WT_REP1.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -425,8 +521,13 @@ "WT_REP2.markdup.sorted.bam", "WT_REP2.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -448,18 +549,23 @@ "RAP1_IAA_30M_REP1.Log.final.out", "RAP1_IAA_30M_REP1.Log.out", "RAP1_IAA_30M_REP1.Log.progress.out", + "RAP1_IAA_30M_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP1.Log.final.out", "RAP1_UNINDUCED_REP1.Log.out", "RAP1_UNINDUCED_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP2.Log.final.out", "RAP1_UNINDUCED_REP2.Log.out", "RAP1_UNINDUCED_REP2.Log.progress.out", + "RAP1_UNINDUCED_REP2.SJ.out.tab", "WT_REP1.Log.final.out", "WT_REP1.Log.out", "WT_REP1.Log.progress.out", + "WT_REP1.SJ.out.tab", "WT_REP2.Log.final.out", "WT_REP2.Log.out", "WT_REP2.Log.progress.out", + "WT_REP2.SJ.out.tab", "picard_metrics", "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -511,30 +617,51 @@ "WT_REP2.sorted.bam.stats", "stringtie", "RAP1_IAA_30M_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_IAA_30M_REP1.coverage.gtf", "RAP1_IAA_30M_REP1.gene.abundance.txt", "RAP1_IAA_30M_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP1.coverage.gtf", "RAP1_UNINDUCED_REP1.gene.abundance.txt", "RAP1_UNINDUCED_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP2.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP2.coverage.gtf", "RAP1_UNINDUCED_REP2.gene.abundance.txt", "RAP1_UNINDUCED_REP2.transcripts.gtf", "WT_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "WT_REP1.coverage.gtf", "WT_REP1.gene.abundance.txt", "WT_REP1.transcripts.gtf", "WT_REP2.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "WT_REP2.coverage.gtf", "WT_REP2.gene.abundance.txt", "WT_REP2.transcripts.gtf", + "tx2gene.tsv", "trimgalore", "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", @@ -677,6 +804,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T11:04:14.333102" + "timestamp": "2024-09-19T19:46:49.794228" } } \ No newline at end of file diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index 646381674..4bc535f7f 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + // All stable path name + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 8c091316e..8591548f9 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -142,6 +142,8 @@ "WT_REP2.stats.txt", "custom", "out", + "genome_gfp.fasta", + "genome_gfp.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw_1_fastqc.html", @@ -164,12 +166,25 @@ "star_salmon", "multiqc_report.html", "multiqc_report_data", + "fastqc-status-check-heatmap.txt", + "fastqc_adapter_content_plot.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", + "multiqc_citations.txt", "multiqc_data.json", "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", + "multiqc_fastqc_fastqc_raw.txt", + "multiqc_featurecounts_biotype_plot.txt", "multiqc_general_stats.txt", "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", @@ -184,6 +199,7 @@ "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", + "multiqc_samtools_idxstats.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", @@ -195,9 +211,16 @@ "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", "picard_deduplication.txt", + "picard_histogram.txt", + "picard_histogram_1.txt", + "picard_histogram_2.txt", + "qualimap_gene_coverage_profile_Counts.txt", + "qualimap_gene_coverage_profile_Normalised.txt", "qualimap_genomic_origin.txt", + "qualimap_rnaseq_cov_hist.txt", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", + "rseqc_infer_experiment_plot.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", @@ -213,6 +236,9 @@ "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", "star_alignment_plot.txt", @@ -276,17 +302,31 @@ "star_salmon_deseq2_pca-plot.pdf", "star_summary_table.pdf", "png", + "dupradar-section-plot.png", "fail_strand_check_table.png", + "fastqc-status-check-heatmap.png", "fastqc_adapter_content_plot.png", + "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", "fastqc_top_overrepresented_sequences_table.png", + "featurecounts_biotype_plot-cnt.png", + "featurecounts_biotype_plot-pct.png", "general_stats_table.png", "picard_deduplication-cnt.png", "picard_deduplication-pct.png", + "qualimap_gene_coverage_profile_Counts.png", + "qualimap_gene_coverage_profile_Normalised.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", + "rseqc_infer_experiment_plot.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", @@ -298,11 +338,18 @@ "rseqc_junction_saturation_plot_Novel_Junctions.png", "rseqc_read_distribution_plot-cnt.png", "rseqc_read_distribution_plot-pct.png", + "rseqc_read_dups_plot.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png", "samtools-stats-dp.png", "samtools_alignment_plot-cnt.png", "samtools_alignment_plot-pct.png", @@ -373,55 +420,86 @@ "salmon", "RAP1_IAA_30M_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "deseq2_qc", + "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -445,13 +523,19 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", + "tx2gene.tsv", "star_salmon", "RAP1_IAA_30M_REP1", "RAP1_IAA_30M_REP1.markdup.sorted.bam", "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -462,8 +546,13 @@ "RAP1_UNINDUCED_REP1.markdup.sorted.bam", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -474,8 +563,13 @@ "RAP1_UNINDUCED_REP2.markdup.sorted.bam", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -486,8 +580,13 @@ "WT_REP1.markdup.sorted.bam", "WT_REP1.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -498,8 +597,13 @@ "WT_REP2.markdup.sorted.bam", "WT_REP2.markdup.sorted.bam.bai", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", "logs", @@ -518,6 +622,7 @@ "WT_REP2.forward.bigWig", "WT_REP2.reverse.bigWig", "deseq2_qc", + "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -537,6 +642,11 @@ "WT_REP1_duprateExpBoxplot.pdf", "WT_REP2_duprateExpBoxplot.pdf", "gene_data", + "RAP1_IAA_30M_REP1_dupMatrix.txt", + "RAP1_UNINDUCED_REP1_dupMatrix.txt", + "RAP1_UNINDUCED_REP2_dupMatrix.txt", + "WT_REP1_dupMatrix.txt", + "WT_REP2_dupMatrix.txt", "histogram", "RAP1_IAA_30M_REP1_expressionHist.pdf", "RAP1_UNINDUCED_REP1_expressionHist.pdf", @@ -544,6 +654,11 @@ "WT_REP1_expressionHist.pdf", "WT_REP2_expressionHist.pdf", "intercepts_slope", + "RAP1_IAA_30M_REP1_intercept_slope.txt", + "RAP1_UNINDUCED_REP1_intercept_slope.txt", + "RAP1_UNINDUCED_REP2_intercept_slope.txt", + "WT_REP1_intercept_slope.txt", + "WT_REP2_intercept_slope.txt", "scatter_plot", "RAP1_IAA_30M_REP1_duprateExpDens.pdf", "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", @@ -551,27 +666,47 @@ "WT_REP1_duprateExpDens.pdf", "WT_REP2_duprateExpDens.pdf", "featurecounts", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv", + "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv", + "RAP1_IAA_30M_REP1.featureCounts.txt", "RAP1_IAA_30M_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv", + "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv", + "RAP1_UNINDUCED_REP1.featureCounts.txt", "RAP1_UNINDUCED_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv", + "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv", + "RAP1_UNINDUCED_REP2.featureCounts.txt", "RAP1_UNINDUCED_REP2.featureCounts.txt.summary", + "WT_REP1.biotype_counts_mqc.tsv", + "WT_REP1.biotype_counts_rrna_mqc.tsv", + "WT_REP1.featureCounts.txt", "WT_REP1.featureCounts.txt.summary", + "WT_REP2.biotype_counts_mqc.tsv", + "WT_REP2.biotype_counts_rrna_mqc.tsv", + "WT_REP2.featureCounts.txt", "WT_REP2.featureCounts.txt.summary", "log", "RAP1_IAA_30M_REP1.Log.final.out", "RAP1_IAA_30M_REP1.Log.out", "RAP1_IAA_30M_REP1.Log.progress.out", + "RAP1_IAA_30M_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP1.Log.final.out", "RAP1_UNINDUCED_REP1.Log.out", "RAP1_UNINDUCED_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP1.SJ.out.tab", "RAP1_UNINDUCED_REP2.Log.final.out", "RAP1_UNINDUCED_REP2.Log.out", "RAP1_UNINDUCED_REP2.Log.progress.out", + "RAP1_UNINDUCED_REP2.SJ.out.tab", "WT_REP1.Log.final.out", "WT_REP1.Log.out", "WT_REP1.Log.progress.out", + "WT_REP1.SJ.out.tab", "WT_REP2.Log.final.out", "WT_REP2.Log.out", "WT_REP2.Log.progress.out", + "WT_REP2.SJ.out.tab", "picard_metrics", "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", "RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -584,90 +719,190 @@ "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "rseqc", "bam_stat", @@ -677,6 +912,11 @@ "WT_REP1.bam_stat.txt", "WT_REP2.bam_stat.txt", "infer_experiment", + "RAP1_IAA_30M_REP1.infer_experiment.txt", + "RAP1_UNINDUCED_REP1.infer_experiment.txt", + "RAP1_UNINDUCED_REP2.infer_experiment.txt", + "WT_REP1.infer_experiment.txt", + "WT_REP2.infer_experiment.txt", "inner_distance", "pdf", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", @@ -825,30 +1065,51 @@ "WT_REP2.sorted.bam.stats", "stringtie", "RAP1_IAA_30M_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_IAA_30M_REP1.coverage.gtf", "RAP1_IAA_30M_REP1.gene.abundance.txt", "RAP1_IAA_30M_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP1.coverage.gtf", "RAP1_UNINDUCED_REP1.gene.abundance.txt", "RAP1_UNINDUCED_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP2.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP2.coverage.gtf", "RAP1_UNINDUCED_REP2.gene.abundance.txt", "RAP1_UNINDUCED_REP2.transcripts.gtf", "WT_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "WT_REP1.coverage.gtf", "WT_REP1.gene.abundance.txt", "WT_REP1.transcripts.gtf", "WT_REP2.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "WT_REP2.coverage.gtf", "WT_REP2.gene.abundance.txt", - "WT_REP2.transcripts.gtf" + "WT_REP2.transcripts.gtf", + "tx2gene.tsv" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -1118,6 +1379,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T19:30:48.005426" + "timestamp": "2024-09-19T19:54:39.111945" } } \ No newline at end of file diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 804808e18..69caa48af 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + // All stable path name + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - (path_name_stable - path_snapshottable).collect{file -> file.getName()}, + // All stable path name + path_name_stable.collect{file -> file.getName()}, // All files with stable contents path_snapshottable ).match() } diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index ea0b5a1e4..c9881f337 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -146,6 +146,8 @@ "WT_REP2.stats.txt", "custom", "out", + "genome_gfp.fasta", + "genome_gfp.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw_1_fastqc.html", @@ -185,13 +187,41 @@ "star_rsem", "multiqc_report.html", "multiqc_report_data", + "cutadapt_filtered_reads_plot.txt", + "cutadapt_trimmed_sequences_plot_3_Counts.txt", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "fastqc-status-check-heatmap-1.txt", + "fastqc-status-check-heatmap.txt", + "fastqc_adapter_content_plot.txt", + "fastqc_overrepresented_sequences_plot-1.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot-1.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot-1.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot-1.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot-1.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot-1.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", + "multiqc_citations.txt", + "multiqc_cutadapt.txt", "multiqc_data.json", "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", + "multiqc_fastqc_fastqc_raw.txt", + "multiqc_fastqc_fastqc_trimmed.txt", + "multiqc_featurecounts_biotype_plot.txt", "multiqc_general_stats.txt", "multiqc_picard_dups.txt", "multiqc_rsem.txt", @@ -207,6 +237,7 @@ "multiqc_salmon_deseq2_clustering-plot_4.txt", "multiqc_salmon_deseq2_pca-plot.txt", "multiqc_samtools_flagstat.txt", + "multiqc_samtools_idxstats.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", @@ -215,12 +246,20 @@ "multiqc_star_rsem_deseq2_clustering-plot_2.txt", "multiqc_star_rsem_deseq2_clustering-plot_3.txt", "multiqc_star_rsem_deseq2_clustering-plot_4.txt", + "multiqc_star_rsem_deseq2_pca-plot.txt", "picard_deduplication.txt", + "picard_histogram.txt", + "picard_histogram_1.txt", + "picard_histogram_2.txt", + "qualimap_gene_coverage_profile_Counts.txt", + "qualimap_gene_coverage_profile_Normalised.txt", "qualimap_genomic_origin.txt", + "qualimap_rnaseq_cov_hist.txt", "qualimap_rnaseq_genome_results.txt", "rsem_assignment_plot.txt", "rsem_multimapping_rates.txt", "rseqc_bam_stat.txt", + "rseqc_infer_experiment_plot.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", @@ -236,6 +275,9 @@ "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", "samtools-stats-dp.txt", "samtools_alignment_plot.txt", "multiqc_report_plots", @@ -313,23 +355,50 @@ "star_rsem_deseq2_clustering-plot.pdf", "star_rsem_deseq2_pca-plot.pdf", "png", + "cutadapt_filtered_reads_plot-cnt.png", + "cutadapt_filtered_reads_plot-pct.png", + "cutadapt_trimmed_sequences_plot_3_Counts.png", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "dupradar-section-plot.png", "fail_strand_check_table.png", + "fastqc-status-check-heatmap-1.png", + "fastqc-status-check-heatmap.png", "fastqc_adapter_content_plot.png", + "fastqc_overrepresented_sequences_plot-1.png", + "fastqc_overrepresented_sequences_plot.png", "fastqc_per_base_n_content_plot-1.png", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot-1.png", "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot-1_Counts.png", + "fastqc_per_sequence_gc_content_plot-1_Percentages.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot-1.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-1-cnt.png", + "fastqc_sequence_counts_plot-1-pct.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot-1.png", + "fastqc_sequence_duplication_levels_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", + "featurecounts_biotype_plot-cnt.png", + "featurecounts_biotype_plot-pct.png", "general_stats_table.png", "picard_deduplication-cnt.png", "picard_deduplication-pct.png", + "qualimap_gene_coverage_profile_Counts.png", + "qualimap_gene_coverage_profile_Normalised.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rsem_assignment_plot-cnt.png", "rsem_assignment_plot-pct.png", + "rsem_multimapping_rates.png", "rseqc_bam_stat.png", + "rseqc_infer_experiment_plot.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", @@ -341,11 +410,18 @@ "rseqc_junction_saturation_plot_Novel_Junctions.png", "rseqc_read_distribution_plot-cnt.png", "rseqc_read_distribution_plot-pct.png", + "rseqc_read_dups_plot.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png", "samtools-stats-dp.png", "samtools_alignment_plot-cnt.png", "samtools_alignment_plot-pct.png", @@ -429,55 +505,86 @@ "salmon", "RAP1_IAA_30M_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "RAP1_UNINDUCED_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP1", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "WT_REP2", "aux_info", + "ambig_info.tsv", + "expected_bias.gz", "fld.gz", "meta_info.json", + "observed_bias.gz", + "observed_bias_3p.gz", + "cmd_info.json", "libParams", "flenDist.txt", + "lib_format_counts.json", "logs", "salmon_quant.log", "quant.genes.sf", "quant.sf", "deseq2_qc", + "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -501,6 +608,7 @@ "salmon.merged.transcript_counts.tsv", "salmon.merged.transcript_lengths.tsv", "salmon.merged.transcript_tpm.tsv", + "tx2gene.tsv", "star_rsem", "RAP1_IAA_30M_REP1.genes.results", "RAP1_IAA_30M_REP1.isoforms.results", @@ -554,6 +662,7 @@ "WT_REP2.forward.bigWig", "WT_REP2.reverse.bigWig", "deseq2_qc", + "R_sessionInfo.log", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -573,6 +682,11 @@ "WT_REP1_duprateExpBoxplot.pdf", "WT_REP2_duprateExpBoxplot.pdf", "gene_data", + "RAP1_IAA_30M_REP1_dupMatrix.txt", + "RAP1_UNINDUCED_REP1_dupMatrix.txt", + "RAP1_UNINDUCED_REP2_dupMatrix.txt", + "WT_REP1_dupMatrix.txt", + "WT_REP2_dupMatrix.txt", "histogram", "RAP1_IAA_30M_REP1_expressionHist.pdf", "RAP1_UNINDUCED_REP1_expressionHist.pdf", @@ -580,6 +694,11 @@ "WT_REP1_expressionHist.pdf", "WT_REP2_expressionHist.pdf", "intercepts_slope", + "RAP1_IAA_30M_REP1_intercept_slope.txt", + "RAP1_UNINDUCED_REP1_intercept_slope.txt", + "RAP1_UNINDUCED_REP2_intercept_slope.txt", + "WT_REP1_intercept_slope.txt", + "WT_REP2_intercept_slope.txt", "scatter_plot", "RAP1_IAA_30M_REP1_duprateExpDens.pdf", "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", @@ -587,10 +706,25 @@ "WT_REP1_duprateExpDens.pdf", "WT_REP2_duprateExpDens.pdf", "featurecounts", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv", + "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv", + "RAP1_IAA_30M_REP1.featureCounts.txt", "RAP1_IAA_30M_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv", + "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv", + "RAP1_UNINDUCED_REP1.featureCounts.txt", "RAP1_UNINDUCED_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv", + "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv", + "RAP1_UNINDUCED_REP2.featureCounts.txt", "RAP1_UNINDUCED_REP2.featureCounts.txt.summary", + "WT_REP1.biotype_counts_mqc.tsv", + "WT_REP1.biotype_counts_rrna_mqc.tsv", + "WT_REP1.featureCounts.txt", "WT_REP1.featureCounts.txt.summary", + "WT_REP2.biotype_counts_mqc.tsv", + "WT_REP2.biotype_counts_rrna_mqc.tsv", + "WT_REP2.featureCounts.txt", "WT_REP2.featureCounts.txt.summary", "log", "RAP1_IAA_30M_REP1.log", @@ -610,91 +744,195 @@ "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "RAP1_UNINDUCED_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP1", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", "WT_REP2", "css", "agogo.css", "ajax-loader.gif", "basic.css", + "bgfooter.png", + "bgtop.png", + "comment-bright.png", + "comment-close.png", + "comment.png", "doctools.js", + "down-pressed.png", + "down.png", + "file.png", "jquery.js", + "minus.png", + "plus.png", "pygments.css", + "qualimap_logo_small.png", "report.css", "searchtools.js", "underscore.js", + "up-pressed.png", + "up.png", "websupport.js", "images_qualimapReport", + "Coverage Profile Along Genes (High).png", + "Coverage Profile Along Genes (Low).png", + "Coverage Profile Along Genes (Total).png", "Junction Analysis.png", "Reads Genomic Origin.png", + "Transcript coverage histogram.png", "qualimapReport.html", "raw_data_qualimapReport", + "coverage_profile_along_genes_(high).txt", + "coverage_profile_along_genes_(low).txt", + "coverage_profile_along_genes_(total).txt", "rnaseq_qc_results.txt", + "rsem.merged.gene_counts.tsv", + "rsem.merged.gene_tpm.tsv", + "rsem.merged.transcript_counts.tsv", + "rsem.merged.transcript_tpm.tsv", "rseqc", "bam_stat", "RAP1_IAA_30M_REP1.bam_stat.txt", @@ -703,6 +941,11 @@ "WT_REP1.bam_stat.txt", "WT_REP2.bam_stat.txt", "infer_experiment", + "RAP1_IAA_30M_REP1.infer_experiment.txt", + "RAP1_UNINDUCED_REP1.infer_experiment.txt", + "RAP1_UNINDUCED_REP2.infer_experiment.txt", + "WT_REP1.infer_experiment.txt", + "WT_REP2.infer_experiment.txt", "inner_distance", "pdf", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", @@ -839,26 +1082,46 @@ "WT_REP2.sorted.bam.stats", "stringtie", "RAP1_IAA_30M_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_IAA_30M_REP1.coverage.gtf", "RAP1_IAA_30M_REP1.gene.abundance.txt", "RAP1_IAA_30M_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP1.coverage.gtf", "RAP1_UNINDUCED_REP1.gene.abundance.txt", "RAP1_UNINDUCED_REP1.transcripts.gtf", "RAP1_UNINDUCED_REP2.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "RAP1_UNINDUCED_REP2.coverage.gtf", "RAP1_UNINDUCED_REP2.gene.abundance.txt", "RAP1_UNINDUCED_REP2.transcripts.gtf", "WT_REP1.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "WT_REP1.coverage.gtf", "WT_REP1.gene.abundance.txt", "WT_REP1.transcripts.gtf", "WT_REP2.ballgown", + "e2t.ctab", + "e_data.ctab", + "i2t.ctab", + "i_data.ctab", "t_data.ctab", "WT_REP2.coverage.gtf", "WT_REP2.gene.abundance.txt", @@ -1143,7 +1406,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T11:19:40.881884" + "timestamp": "2024-09-19T20:00:49.243637" }, "Params: --aligner star_rsem - stub": { "content": [ @@ -1193,6 +1456,8 @@ [ "custom", "out", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", "fastqc", "raw", "RAP1_IAA_30M_REP1_raw.html", @@ -1232,6 +1497,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-17T19:41:35.156352" + "timestamp": "2024-09-19T20:01:39.319147" } } \ No newline at end of file From 8550e6d8df4ff97617d41ae1b19d03e17c5930f5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 20 Sep 2024 08:41:43 +0200 Subject: [PATCH 075/100] code polish --- tests/default.nf.test | 28 +++++++++++++------------- tests/featurecounts_group_type.nf.test | 24 +++++++++++----------- tests/hisat2.nf.test | 24 +++++++++++----------- tests/kallisto.nf.test | 24 +++++++++++----------- tests/min_mapped_reads.nf.test | 24 +++++++++++----------- tests/remove_ribo_rna.nf.test | 24 +++++++++++----------- tests/salmon.nf.test | 24 +++++++++++----------- tests/skip_qc.nf.test | 24 +++++++++++----------- tests/skip_trimming.nf.test | 12 +++++------ tests/star_rsem.nf.test | 24 +++++++++++----------- 10 files changed, 116 insertions(+), 116 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 6763d799f..c8e21adea 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -12,10 +12,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -23,10 +23,10 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - path_name_stable.collect{file -> file.getName()}, + // All stable path name + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } @@ -43,10 +43,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -54,10 +54,10 @@ nextflow_pipeline { workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name from which we remove files with stable contents - path_name_stable.collect{file -> file.getName()}, + // All stable path name + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index 0323dab87..af3173caa 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -13,10 +13,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -25,9 +25,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - path_name_stable.collect{file -> file.getName()}, + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } @@ -45,10 +45,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -57,9 +57,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - path_name_stable.collect{file -> file.getName()}, + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 9cbb2e1aa..1ac43faa9 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -13,10 +13,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -25,9 +25,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - path_name_stable.collect{file -> file.getName()}, + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } @@ -45,10 +45,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -57,9 +57,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - path_name_stable.collect{file -> file.getName()}, + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index ee9b7c50e..272ae0351 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -15,10 +15,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -27,9 +27,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - path_name_stable.collect{file -> file.getName()}, + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } @@ -49,10 +49,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -61,9 +61,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - path_name_stable.collect{file -> file.getName()}, + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index 080dc70fe..b0d6bdc1d 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -13,10 +13,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -25,9 +25,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - path_name_stable.collect{file -> file.getName()}, + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } @@ -45,10 +45,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -57,9 +57,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - path_name_stable.collect{file -> file.getName()}, + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index 1766dbdf6..d5a12272a 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -13,10 +13,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -25,9 +25,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - path_name_stable.collect{file -> file.getName()}, + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } @@ -45,10 +45,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -57,9 +57,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - path_name_stable.collect{file -> file.getName()}, + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index d051dddb3..11bc250bf 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -15,10 +15,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -27,9 +27,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - path_name_stable.collect{file -> file.getName()}, + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } @@ -49,10 +49,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -61,9 +61,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - path_name_stable.collect{file -> file.getName()}, + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index 64eae6885..8c2ab20fe 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -13,10 +13,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -25,9 +25,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - path_name_stable.collect{file -> file.getName()}, + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } @@ -45,10 +45,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -57,9 +57,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - path_name_stable.collect{file -> file.getName()}, + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index 4bc535f7f..045a4b590 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -13,10 +13,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -25,9 +25,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - path_name_stable.collect{file -> file.getName()}, + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 69caa48af..3c54a45d1 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -13,10 +13,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -25,9 +25,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - path_name_stable.collect{file -> file.getName()}, + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } @@ -45,10 +45,10 @@ nextflow_pipeline { } then { - // path_name_stable: All files + folders in ${params.outdir}/ with a stable name - def path_name_stable = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) - // path_snapshottable: All files in ${params.outdir}/ with stable content - def path_snapshottable = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) assertAll( { assert workflow.success}, { assert snapshot( @@ -57,9 +57,9 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - path_name_stable.collect{file -> file.getName()}, + stable_name.*name, // All files with stable contents - path_snapshottable + stable_path ).match() } ) } From 5a62a0f02878cb03cf6df1f10cfaa353a5fa6435 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 20 Sep 2024 08:52:12 +0200 Subject: [PATCH 076/100] typo --- tests/default.nf.test | 4 ++-- tests/featurecounts_group_type.nf.test | 4 ++-- tests/hisat2.nf.test | 4 ++-- tests/kallisto.nf.test | 4 ++-- tests/min_mapped_reads.nf.test | 4 ++-- tests/remove_ribo_rna.nf.test | 4 ++-- tests/salmon.nf.test | 4 ++-- tests/skip_qc.nf.test | 4 ++-- tests/skip_trimming.nf.test | 2 +- tests/star_rsem.nf.test | 4 ++-- 10 files changed, 19 insertions(+), 19 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index c8e21adea..6337bb996 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -24,7 +24,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } @@ -55,7 +55,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index af3173caa..d8972ebf5 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -25,7 +25,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } @@ -57,7 +57,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 1ac43faa9..c1c90c391 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -25,7 +25,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } @@ -57,7 +57,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index 272ae0351..dd2c316c8 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -27,7 +27,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } @@ -61,7 +61,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index b0d6bdc1d..f7a5fdae8 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -25,7 +25,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } @@ -57,7 +57,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index d5a12272a..729fb2c4e 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -25,7 +25,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } @@ -57,7 +57,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index 11bc250bf..bbf4a9102 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -27,7 +27,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } @@ -61,7 +61,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index 8c2ab20fe..5fb8bb370 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -25,7 +25,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } @@ -57,7 +57,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index 045a4b590..bb5c44463 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -25,7 +25,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 3c54a45d1..837554c39 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -25,7 +25,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } @@ -57,7 +57,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name - stable_name.*name, + stable_name*.name, // All files with stable contents stable_path ).match() } From 82c833d427c21d9d9e44fa8cc94b8b6c9bfb0785 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Fri, 20 Sep 2024 16:51:51 +0200 Subject: [PATCH 077/100] Apply suggestions from code review --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9029fe352..f2b29a63f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v3.16.0dev - [date] - ### Enhancements & fixes - [PR #1376](https://github.com/nf-core/rnaseq/pull/1376) - Fix invalid named parameter syntax From f5f055e99e5495fbaf0036fdbf34d9bb294a55e9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 20 Sep 2024 16:54:29 +0200 Subject: [PATCH 078/100] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6558baf06..b28330310 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #1388](https://github.com/nf-core/rnaseq/pull/1351) - Adding Kraken2/Bracken on unaligned reads as an additional quality control step to detect sample contamination - [PR #1186](https://github.com/nf-core/rnaseq/pull/1186) - Bump pipeline version to 3.16.0dev +- [PR #1389](https://github.com/nf-core/rnaseq/pull/1389) - Update animated subway map ### Parameters From 577c3aba246933cc393a77b727aadf30c2e22513 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 20 Sep 2024 17:34:48 +0200 Subject: [PATCH 079/100] update animated metro_map --- docs/images/nf-core-rnaseq_metro_map_grey.png | Bin 302024 -> 300595 bytes docs/images/nf-core-rnaseq_metro_map_grey.svg | 9033 ++++++++++++----- ...nf-core-rnaseq_metro_map_grey_animated.svg | 4238 +++++++- 3 files changed, 10283 insertions(+), 2988 deletions(-) diff --git a/docs/images/nf-core-rnaseq_metro_map_grey.png b/docs/images/nf-core-rnaseq_metro_map_grey.png index 1cb1cf32fbda99a04329aec503721f2cbff98b0b..79b4e2afc5574e118546b6a346d43cbc8de73ee1 100644 GIT binary patch literal 300595 zcmeFZgG3@0{S&_H`u64Xs2um&Yt4Db7~>vud&x?R;bIeGqfjVZ^dk{@6bfq)g~H6oItxD$ 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Genome alignment & quantification3. Pseudo-alignment & quantification1. Pre-processing4. Post-processingRSeQC(multiple modules)Kraken2/Bracken3SalmonKallistoMultiQCTSV54SAMtools(sort, index, stats)BEDtoolsgenomecov GermlineSarek  Exome GermlineSarek  Exome GermlineSarek  ExomeHTML GermlineSarek 1catfastqSTAGE2. Genome alignment & quantification3. Pseudo-alignment & quantification1. Pre-processing4. Post-processing35412 +  GermlineSarek  Exome GermlineSarek TSV Exome diff --git a/docs/images/nf-core-rnaseq_metro_map_grey_animated.svg b/docs/images/nf-core-rnaseq_metro_map_grey_animated.svg index 96ea8972a..8886dd962 100644 --- a/docs/images/nf-core-rnaseq_metro_map_grey_animated.svg +++ b/docs/images/nf-core-rnaseq_metro_map_grey_animated.svg @@ -21,7 +21,12 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:cc="http://creativecommons.org/ns#" xmlns:dc="http://purl.org/dc/elements/1.1/">5 + href="#hisat2_trimgalore" /> + href="#hisat2_fastp" /> + href="#hisat2_trimgalore" /> + href="#hisat2_fastp" /> + id="text74" + style="font-size:76.4916px;line-height:1;font-family:'DejaVu Sans Mono';-inkscape-font-specification:'DejaVu Sans Mono';white-space:pre;fill:#ffffff;stroke-width:15.1181;stroke-linecap:round;stroke-linejoin:round" + transform="matrix(0.09223963,0,0,0.09223963,199.99988,-1.0793955)" + aria-label="Kraken2/ Bracken"> From 712342aa3f9218eb0b46c90b4423eaf6778499ad Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 20 Sep 2024 17:53:59 +0200 Subject: [PATCH 080/100] no snpashots of tasks size for workflow for remove_ribo_rna --- tests/remove_ribo_rna.nf.test | 3 ++- tests/remove_ribo_rna.nf.test.snap | 3 +-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index 729fb2c4e..287256e0a 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -21,7 +21,8 @@ nextflow_pipeline { { assert workflow.success}, { assert snapshot( // Number of tasks - workflow.trace.tasks().size(), + // Not snapshoting number of tasks as one task fails and gets retried quite often + // workflow.trace.tasks().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index a80ccee83..8a6c81eda 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -1,7 +1,6 @@ { "Params: --remove_ribo_rna": { "content": [ - 207, { "BBMAP_BBSPLIT": { "bbmap": 39.01 @@ -1620,4 +1619,4 @@ }, "timestamp": "2024-09-19T19:37:24.981917" } -} \ No newline at end of file +} From 5bd3d87e6f644ea49652cce547a248b1bef6df94 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 23 Sep 2024 10:41:15 +0200 Subject: [PATCH 081/100] snapshot number of sucessful tasks --- tests/default.nf.test | 4 ++-- tests/hisat2.nf.test | 8 ++++---- tests/kallisto.nf.test | 8 ++++---- tests/min_mapped_reads.nf.test | 8 ++++---- tests/remove_ribo_rna.nf.test | 9 ++++----- tests/remove_ribo_rna.nf.test.snap | 1 + tests/salmon.nf.test | 8 ++++---- tests/skip_qc.nf.test | 8 ++++---- tests/skip_trimming.nf.test | 4 ++-- tests/star_rsem.nf.test | 8 ++++---- 10 files changed, 33 insertions(+), 33 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 6337bb996..64b80ae56 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -50,8 +50,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index c1c90c391..25b5a83ab 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -20,8 +20,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name @@ -52,8 +52,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index dd2c316c8..8398a01a4 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -22,8 +22,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name @@ -56,8 +56,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index f7a5fdae8..f05b94796 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -20,8 +20,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name @@ -52,8 +52,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index 287256e0a..14a65e9eb 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -20,9 +20,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - // Not snapshoting number of tasks as one task fails and gets retried quite often - // workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name @@ -53,8 +52,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 8a6c81eda..ad5b3e2a6 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -1,6 +1,7 @@ { "Params: --remove_ribo_rna": { "content": [ + 207, { "BBMAP_BBSPLIT": { "bbmap": 39.01 diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index bbf4a9102..a30fa248c 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -22,8 +22,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name @@ -56,8 +56,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index 5fb8bb370..e996e8d4c 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -20,8 +20,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name @@ -52,8 +52,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index bb5c44463..4dc4cb54e 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -20,8 +20,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 837554c39..6beb1804d 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -20,8 +20,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name @@ -52,8 +52,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name From 0df09952baff0fbb63825c3904206973ab1ed899 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 23 Sep 2024 10:59:49 +0200 Subject: [PATCH 082/100] typo --- tests/remove_ribo_rna.nf.test.snap | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index ad5b3e2a6..6e506b035 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -1,7 +1,7 @@ { "Params: --remove_ribo_rna": { "content": [ - 207, + 205, { "BBMAP_BBSPLIT": { "bbmap": 39.01 From b21e93c4acc828b72343b75f2e9d5c900e691002 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 23 Sep 2024 11:19:04 +0200 Subject: [PATCH 083/100] Update tests/featurecounts_group_type.nf.test --- tests/featurecounts_group_type.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index d8972ebf5..0052d64eb 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -1,6 +1,6 @@ nextflow_pipeline { - name "Test pipeline wjava.lang.String(ithout) a group type for featureCounts" + name "Test pipeline without a group type for featureCounts" script "../main.nf" test("Params: --featurecounts_group_type false") { From 8dc2d34faaff320e84b93f5f26a25fd92c8fb7e8 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 23 Sep 2024 11:21:21 +0200 Subject: [PATCH 084/100] why was this not commited? --- tests/default.nf.test | 4 ++-- tests/featurecounts_group_type.nf.test | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 64b80ae56..d51a3fbf6 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -19,8 +19,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index 0052d64eb..f18d89b57 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -20,8 +20,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name @@ -52,8 +52,8 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of tasks - workflow.trace.tasks().size(), + // Number of successful tasks + workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name From f6522c801ad9884b49f5ddc02e18486e6caba86b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 30 Sep 2024 14:43:47 +0200 Subject: [PATCH 085/100] patch bedtools/genomecov to use quay.io to solve issue with nf-core download --- CHANGELOG.md | 1 + modules.json | 3 +- .../genomecov/bedtools-genomecov.diff | 37 +++++++++++++++++++ modules/nf-core/bedtools/genomecov/main.nf | 4 +- 4 files changed, 41 insertions(+), 4 deletions(-) create mode 100644 modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff diff --git a/CHANGELOG.md b/CHANGELOG.md index d2797457d..a4adf8bdb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #1386](https://github.com/nf-core/rnaseq/pull/1386) - Bump pipeline version to 3.16.0dev - [PR #1388](https://github.com/nf-core/rnaseq/pull/1388) - Adding Kraken2/Bracken on unaligned reads as an additional quality control step to detect sample contamination - [PR #1389](https://github.com/nf-core/rnaseq/pull/1389) - Update animated subway map +- [PR #1393](https://github.com/nf-core/rnaseq/pull/1393) - Use quay.io for bedtools/genomecov to solve issue with nf-core download ### Parameters diff --git a/modules.json b/modules.json index 4c9ba76f1..c351786e2 100644 --- a/modules.json +++ b/modules.json @@ -13,7 +13,8 @@ "bedtools/genomecov": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff" }, "bracken/bracken": { "branch": "master", diff --git a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff new file mode 100644 index 000000000..02fdbd053 --- /dev/null +++ b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff @@ -0,0 +1,37 @@ +Changes in module 'nf-core/bedtools/genomecov' +Changes in 'bedtools/genomecov/main.nf': +--- modules/nf-core/bedtools/genomecov/main.nf ++++ modules/nf-core/bedtools/genomecov/main.nf +@@ -3,9 +3,7 @@ + label 'process_single' + + conda "${moduleDir}/environment.yml" +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'oras://community.wave.seqera.io/library/bedtools_coreutils:ba273c06a3909a15': +- 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }" ++ container 'nf-core/bedtools_coreutils:a623c13f66d5262b' + + input: + tuple val(meta), path(intervals), val(scale) + +'modules/nf-core/bedtools/genomecov/meta.yml' is unchanged +'modules/nf-core/bedtools/genomecov/environment.yml' is unchanged +'modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap' is unchanged +'modules/nf-core/bedtools/genomecov/tests/nextflow.config' is unchanged +Changes in 'bedtools/genomecov/tests/main.nf.test': +--- modules/nf-core/bedtools/genomecov/tests/main.nf.test ++++ modules/nf-core/bedtools/genomecov/tests/main.nf.test +@@ -3,11 +3,6 @@ + script "../main.nf" + process "BEDTOOLS_GENOMECOV" + config "./nextflow.config" +- +- tag "modules" +- tag "modules_nfcore" +- tag "bedtools" +- tag "bedtools/genomecov" + + test("sarscov2 - no scale") { + when { + +************************************************************ diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 8403c5303..10a99d439 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -3,9 +3,7 @@ process BEDTOOLS_GENOMECOV { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/bedtools_coreutils:ba273c06a3909a15': - 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }" + container 'nf-core/bedtools_coreutils:a623c13f66d5262b' input: tuple val(meta), path(intervals), val(scale) From 5c61ed3490988b384beae45e3e73609b7974924f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 30 Sep 2024 14:50:50 +0200 Subject: [PATCH 086/100] use url for singularity --- .../nf-core/bedtools/genomecov/bedtools-genomecov.diff | 8 ++++---- modules/nf-core/bedtools/genomecov/main.nf | 4 +++- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff index 02fdbd053..6475cdda5 100644 --- a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff +++ b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff @@ -2,14 +2,14 @@ Changes in module 'nf-core/bedtools/genomecov' Changes in 'bedtools/genomecov/main.nf': --- modules/nf-core/bedtools/genomecov/main.nf +++ modules/nf-core/bedtools/genomecov/main.nf -@@ -3,9 +3,7 @@ - label 'process_single' +@@ -4,8 +4,8 @@ conda "${moduleDir}/environment.yml" -- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/bedtools_coreutils:ba273c06a3909a15': - 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }" -+ container 'nf-core/bedtools_coreutils:a623c13f66d5262b' ++ 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21': ++ 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" input: tuple val(meta), path(intervals), val(scale) diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 10a99d439..60d7d9e20 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -3,7 +3,9 @@ process BEDTOOLS_GENOMECOV { label 'process_single' conda "${moduleDir}/environment.yml" - container 'nf-core/bedtools_coreutils:a623c13f66d5262b' + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21': + 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" input: tuple val(meta), path(intervals), val(scale) From 894a770a06b3f09f7f8188f3505e88578605c01d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 30 Sep 2024 14:53:01 +0200 Subject: [PATCH 087/100] use proper url for singularity --- modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff | 2 +- modules/nf-core/bedtools/genomecov/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff index 6475cdda5..53d7e34df 100644 --- a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff +++ b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff @@ -8,7 +8,7 @@ Changes in 'bedtools/genomecov/main.nf': container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/bedtools_coreutils:ba273c06a3909a15': - 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }" -+ 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21': ++ 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': + 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" input: diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 60d7d9e20..91869ec23 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -4,7 +4,7 @@ process BEDTOOLS_GENOMECOV { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21': + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" input: From 30483c77ccca902b14e5dec6223c2d84861f3ed9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 30 Sep 2024 19:09:00 +0200 Subject: [PATCH 088/100] prepare RC 3.15.2 --- CHANGELOG.md | 15 ++++++++++++++- nextflow.config | 2 +- .../rnaseq/assets/multiqc/multiqc_config.yml | 2 +- 3 files changed, 16 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a4adf8bdb..a87075994 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v3.16.0dev - [date] +## [[3.15.2](https://github.com/nf-core/rnaseq/releases/tag/3.15.2)] - 2024-10-01 ### Enhancements & fixes @@ -40,6 +40,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 > > **NB:** Dependency has been **removed** if new version information isn't present. +### Credits + +Special thanks to the following for their contributions to the release: + +- [Adam Talbot](https://github.com/adamrtalbot) +- [Ezra Greenberg](https://github.com/egreenberg7) +- [Jonathan Manning](https://github.com/pinin4fjords) +- [Matthias Zepper](https://github.com/MatthiasZepper) +- [Maxime Garcia](https://github.com/maxulysse) +- [Paolo Di Tommaso](https://github.com/pditommaso) +- [Phil Ewels](https://github.com/ewels) +- [Shaun Regenbaum](https://github.com/Shaun-Regenbaum) + ## [[3.15.1](https://github.com/nf-core/rnaseq/releases/tag/3.15.1)] - 2024-09-16 ### Enhancements & fixes diff --git a/nextflow.config b/nextflow.config index 94481109e..6d58c9224 100644 --- a/nextflow.config +++ b/nextflow.config @@ -345,7 +345,7 @@ manifest { description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '3.16.0dev' + version = '3.15.2' doi = 'https://doi.org/10.5281/zenodo.1400710' } diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml index 63fad09f1..b8dbc608d 100644 --- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml +++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation. + This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: # Important checks and failures sample-status: From 1424156620f93c53b8d184e7f7844010afcb02de Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 30 Sep 2024 19:22:30 +0200 Subject: [PATCH 089/100] update version in snapshots too --- tests/default.nf.test.snap | 4 ++-- tests/featurecounts_group_type.nf.test.snap | 4 ++-- tests/hisat2.nf.test.snap | 4 ++-- tests/kallisto.nf.test.snap | 4 ++-- tests/min_mapped_reads.nf.test.snap | 4 ++-- tests/remove_ribo_rna.nf.test.snap | 4 ++-- tests/salmon.nf.test.snap | 4 ++-- tests/skip_qc.nf.test.snap | 4 ++-- tests/skip_trimming.nf.test.snap | 2 +- tests/star_rsem.nf.test.snap | 4 ++-- 10 files changed, 19 insertions(+), 19 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 79b3ca290..78107dc37 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -266,7 +266,7 @@ }, "Params: default - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -932,7 +932,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 3a08ab907..13c036a1c 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -747,7 +747,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" ], "meta": { "nf-test": "0.9.0", @@ -757,7 +757,7 @@ }, "Params: --featurecounts_group_type false - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 1a15dd9a4..3c7e95bb3 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -631,7 +631,7 @@ }, "Params: --aligner hisat2 - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -726,7 +726,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_ALIGN={hisat2=2.2.1, samtools=1.16.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, 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UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, KALLISTO_QUANT={kallisto=0.48.0}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" ], "meta": { "nf-test": "0.9.0", @@ -219,7 +219,7 @@ }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, 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gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, SORTMERNA={sortmerna=4.3.6}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 004c15ad4..e4d4fd48c 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -61,7 +61,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" ], "meta": { "nf-test": "0.9.0", @@ -265,7 +265,7 @@ }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 7a1eaccf3..7cba6b400 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -157,7 +157,7 @@ }, "Params: --skip_qc - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -477,7 +477,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 0cced5ad5..dff48a776 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -751,7 +751,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index a6a804341..9377ad70d 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -766,7 +766,7 @@ }, "Params: --aligner star_rsem - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -797,7 +797,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_RSEM={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEM_CALCULATEEXPRESSION={rsem=1.3.1, star=2.7.10a}, RSEM_MERGE_COUNTS={sed=4.7}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_RSEM={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEM_CALCULATEEXPRESSION={rsem=1.3.1, star=2.7.10a}, RSEM_MERGE_COUNTS={sed=4.7}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" ], "meta": { "nf-test": "0.9.0", From 5d79bdc35be00a9f8337ba223d0276d46776879a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 1 Oct 2024 10:49:23 +0200 Subject: [PATCH 090/100] use nft-utils --- nf-test.config | 1 + tests/.nftignore | 131 +++++++++++++++++ tests/default.nf.test | 12 +- tests/featurecounts_group_type.nf.test | 12 +- tests/hisat2.nf.test | 12 +- tests/kallisto.nf.test | 12 +- tests/lib/UTILS.groovy | 23 --- tests/lib/UTILS_PIPELINE.groovy | 186 ------------------------- tests/min_mapped_reads.nf.test | 12 +- tests/remove_ribo_rna.nf.test | 12 +- tests/salmon.nf.test | 12 +- tests/skip_qc.nf.test | 12 +- tests/skip_trimming.nf.test | 6 +- tests/star_rsem.nf.test | 12 +- 14 files changed, 189 insertions(+), 266 deletions(-) create mode 100644 tests/.nftignore delete mode 100644 tests/lib/UTILS.groovy delete mode 100644 tests/lib/UTILS_PIPELINE.groovy diff --git a/nf-test.config b/nf-test.config index 0f4cac519..2f04d4302 100644 --- a/nf-test.config +++ b/nf-test.config @@ -13,5 +13,6 @@ config { // load the necessary plugins plugins { load "nft-bam@0.3.0" + load "nft-utils@0.0.1" } } diff --git a/tests/.nftignore b/tests/.nftignore new file mode 100644 index 000000000..2328576b7 --- /dev/null +++ b/tests/.nftignore @@ -0,0 +1,131 @@ +**/*DupRate_plot.{pdf,r} +**/*Log.{final,progress}.out +**/*bam_stat.txt +**/*coverage.gtf +**/*fastq.gz_trimming_report.txt +**/*featureCounts.txt.summary +**/*gene.abundance.txt +**/*inner_distance* +**/*junction* +**/*markdup.sorted.MarkDuplicates.metrics.txt +**/*markdup.sorted.{bam,bam.bai} +**/*read_distribution.txt +**/*sorted.bam.{flagstat,idxstats,stats} +**/*sortmerna.log +**/*splice_{events,junction}.{pdf,png,svg} +**/*stats.txt +**/*transcripts.gtf +**/*{cnt,model,theta} +**/*{css,gif,js} +**/*{forward,reverse}.bigWig +**/*{genes,isoforms}.results +**/*{pos,seq}.DupRate.xls +**/*_fastqc.{html,zip} +**/*_raw.{html,zip} +**/*_{duprateExpBoxplot,duprateExpDens,expressionHist}.{pdf,png,svg} +**/*hisat2.summary +**/Junction\sAnalysis.png +**/RAP1_IAA_30M_REP1.log +**/RAP1_IAA_30M_REP1.txt +**/RAP1_UNINDUCED_REP1.log +**/RAP1_UNINDUCED_REP1.txt +**/RAP1_UNINDUCED_REP2.log +**/RAP1_UNINDUCED_REP2.txt +**/Reads\sGenomic\sOrigin.png +**/WT_REP1.log +**/WT_REP1.txt +**/WT_REP2.log +**/WT_REP2.txt +**/abundance.{h5,tsv} +**/cutadapt_filtered_reads_plot-{cnt,pct}.{pdf,svg} +**/cutadapt_trimmed_sequences_*{pdf,svg} +**/deseq2* +**/dupradar-section-plot.{pdf,svg} +**/fail_mapped_samples_table* +**/fail_strand_check_table* +**/fastqc-status-check-*{pdf,svg} +**/fastqc_adapter_content_plot.{pdf,png,svg} +**/fastqc_overrepresented_sequences_plot*{pdf,svg} +**/fastqc_per_base_*_plot*{pdf,png,svg} +**/fastqc_per_sequence_*{pdf,svg} +**/fastqc_sequence_length_distribution_plot.{pdf,png,svg} +**/fastqc_sequence_{counts,duplication_levels}_plot*{pdf,svg} +**/fastqc_top_overrepresented_sequences_table*{pdf,png,svg,txt} +**/featurecounts_biotype_plot-{cnt,pct}.{pdf,svg} +**/fld.gz +**/flenDist.txt +**/general_stats_table.{pdf,png,svg} +**/hisat2_pe_plot.txt +**/hisat2_se_plot*{png,svg} +**/hisat2_{pe,se}_plot-{cnt,pct}.{pdf,png,svg} +**/junction_saturation_known.txt +**/junction_saturation_novel.txt +**/kallisto_alignment*{pdf,png,svg} +**/kallisto_alignment.txt +**/kallisto_quant.log +**/meta_info.json +**/multiqc_data.json +**/multiqc_dupradar-section-plot.txt +**/multiqc_fail_strand_check_table.txt +**/multiqc_general_stats.txt +**/multiqc_hisat2.txt +**/multiqc_kallisto.txt +**/multiqc_picard_dups.txt +**/multiqc_plots +**/multiqc_report.html +**/multiqc_rsem.txt +**/multiqc_rseqc_bam_stat.txt +**/multiqc_rseqc_infer_experiment.txt +**/multiqc_rseqc_junction_annotation.txt +**/multiqc_rseqc_read_distribution.txt +**/multiqc_salmon.txt +**/multiqc_samtools_flagstat.txt +**/multiqc_samtools_stats.txt +**/multiqc_software_versions.txt +**/multiqc_sortmerna.txt +**/multiqc_sources.txt +**/multiqc_star.txt +**/multiqc_{salmon,star_salmon}_deseq2_pca-plot*txt +**/picard_deduplication-{cnt,pct}.{pdf,png,svg} +**/picard_deduplication.txt +**/qualimapReport.html +**/qualimap_gene_coverage_profile_Counts.{pdf,svg} +**/qualimap_gene_coverage_profile_Normalised.{pdf,svg} +**/qualimap_genomic_origin-{cnt,pct}.{pdf,png,svg} +**/qualimap_genomic_origin.txt +**/qualimap_rnaseq_genome_results.txt +**/quant.genes.sf +**/quant.sf +**/rnaseq_qc_results.txt +**/rsem_assignment_plot-{cnt,pct}.{pdf,png,svg} +**/rsem_assignment_plot.txt +**/rsem_multimapping_rates.{pdf,svg,txt} +**/rseqc_bam_stat.{pdf,png,svg,txt} +**/rseqc_infer_experiment_plot.{pdf,svg} +**/rseqc_inner_* +**/rseqc_junction_* +**/rseqc_read_distribution_* +**/rseqc_read_dups.txt +**/rseqc_read_dups_plot.txt +**/rseqc_read_dups_plot.{pdf,svg} +**/run_info.json +**/salmon_plot.{pdf,png,svg,txt} +**/salmon_quant.log +**/samtools-flagstat* +**/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.{pdf,svg} +**/samtools-idxstats-mapped-reads-plot_Normalised_Counts-{cnt,pct}.{pdf,svg} +**/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.{pdf,svg} +**/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-{cnt,pct}.{pdf,svg} +**/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.{pdf,svg} +**/samtools-idxstats-mapped-reads-plot_Raw_Counts-{cnt,pct}.{pdf,svg} +**/samtools-stats-dp.{pdf,png,svg,txt} +**/sortmerna-detailed-plot-{cnt,pct}.{pdf,svg} +**/sortmerna-detailed-plot.txt +**/star_summary_table.{pdf,png,svg,txt} +**/t_data.ctab +**/{kallisto,salmon}.merged* +**/*{salmon,star_salmon,star_rsem}_deseq2_clustering-plot*{pdf,png,txt} +**/{salmon,star_rsem}_deseq2_{clustering,pca}-plot.{pdf,png,svg} +**/{salmon,star_rsem}_deseq2_{pca,pca}-plot.{pdf,png,svg} +**/{samtools,star}_alignment_plot* +**/{star_rsem,star_salmon}_deseq2_{clustering,pca}-plot*{pdf,png,svg} diff --git a/tests/default.nf.test b/tests/default.nf.test index d51a3fbf6..1e5c84d4b 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -13,16 +13,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents @@ -44,16 +44,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index f18d89b57..a05949f84 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -14,16 +14,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents @@ -46,16 +46,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 25b5a83ab..ff9e4d99d 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -14,16 +14,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents @@ -46,16 +46,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index 8398a01a4..fed4532f8 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -16,16 +16,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents @@ -50,16 +50,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy deleted file mode 100644 index 48500bd3f..000000000 --- a/tests/lib/UTILS.groovy +++ /dev/null @@ -1,23 +0,0 @@ -class UTILS { - // Remove Nextflow version from pipeline_software_mqc_versions.yml - public static Object removeNextflowVersion(pipeline_software_mqc_versions) { - def softwareVersions = path(pipeline_software_mqc_versions).yaml - if (softwareVersions.containsKey("Workflow")) softwareVersions.Workflow.remove("Nextflow") - return softwareVersions - } - - // Recursively list all files in a directory and its sub-directories, matching or not matching supplied suffixes - public static getAllFilesFromDir(outdir, boolean includeDir = true, List excludeRegexes = null) { - def output = [] - new File(outdir).eachFileRecurse() { file -> - boolean matchesInclusion = includeDir ? true : file.isFile() - boolean matchesExclusion = excludeRegexes ? excludeRegexes.any { regex -> file.name.toString() ==~ regex } : false - - // Add files (or folders if includeDir is set to true) to the list that don't match excludeRegexes - if (matchesInclusion && !matchesExclusion) output.add(file) - } - return output.sort { it.path } - } - // Static (global) exclusion regexes list - static List exclusionRegexesForUnstableFileNames = [/.*\d{4}-\d{2}-\d{2}_\d{2}-\d{2}-\d{2}.*/] -} diff --git a/tests/lib/UTILS_PIPELINE.groovy b/tests/lib/UTILS_PIPELINE.groovy deleted file mode 100644 index 01bf858fe..000000000 --- a/tests/lib/UTILS_PIPELINE.groovy +++ /dev/null @@ -1,186 +0,0 @@ -class UTILS_PIPELINE { - // These are the files to exclude when we want to snapshot - static List exclusionRegexesForUnstableFileContents = [ - // To exclude the pipeline_software_mqc_versions.yml file that contains the Nextflow version - /nf_core_.*_software_mqc_versions\.yml/, - - // To exclude this folder that somehow is a file on stub tests - /multiqc_plots/, - - // To exclude from qualimap css folders - /.*\.(css|gif|js)/, - - // To exclude bbsplit files - /.*\.stats\.txt/, - - // To exclude FASTQC reports - /.*_raw\.(html|zip)/, - /.*_fastqc\.(html|zip)/, - - // To exclude from the MultiQC reports - /cutadapt_filtered_reads_plot-(cnt|pct)\.(pdf|svg)/, - /cutadapt_trimmed_sequences_.*\.(pdf|svg)/, - /dupradar-section-plot\.(pdf|svg)/, - /fail_mapped_samples_table.*/, - /fail_strand_check_table.*/, - /fastqc-status-check-.*\.(pdf|svg)/, - /fastqc_adapter_content_plot\.(pdf|png|svg)/, - /fastqc_overrepresented_sequences_plot(.*)?\.(pdf|svg)/, - /fastqc_per_base_.*_plot(.*)?\.(pdf|png|svg)/, - /fastqc_per_sequence_.*\.(pdf|svg)/, - /fastqc_sequence_(counts|duplication_levels)_plot(.*)?\.(pdf|svg)/, - /fastqc_sequence_length_distribution_plot\.(pdf|png|svg)/, - /fastqc_top_overrepresented_sequences_table(.*)?\.(pdf|png|svg|txt)/, - /featurecounts_biotype_plot-(cnt|pct)\.(pdf|svg)/, - /general_stats_table\.(pdf|png|svg)/, - /hisat2_(pe|se)_plot-(cnt|pct)\.(pdf|png|svg)/, - /hisat2_pe_plot\.txt/, - /hisat2_se_plot.*\.(png|svg)/, - /junction_saturation_known\.txt/, - /junction_saturation_novel\.txt/, - /kallisto_alignment.*.(pdf|png|svg)/, - /kallisto_alignment\.txt/, - /multiqc_data\.json/, - /multiqc_dupradar-section-plot\.txt/, - /multiqc_fail_strand_check_table\.txt/, - /multiqc_general_stats\.txt/, - /multiqc_hisat2\.txt/, - /multiqc_kallisto\.txt/, - /multiqc_picard_dups\.txt/, - /multiqc_report\.html/, - /multiqc_rsem\.txt/, - /multiqc_rseqc_bam_stat\.txt/, - /multiqc_rseqc_infer_experiment\.txt/, - /multiqc_rseqc_junction_annotation\.txt/, - /multiqc_rseqc_read_distribution\.txt/, - /multiqc_salmon\.txt/, - /(multiqc_)?(salmon|star_salmon|star_rsem)_deseq2_clustering-plot(.*)?\.(pdf|png|txt)/, - /multiqc_(salmon|star_salmon)_deseq2_pca-plot.*\.txt/, - /multiqc_samtools_flagstat\.txt/, - /multiqc_samtools_stats\.txt/, - /multiqc_software_versions\.txt/, - /multiqc_sortmerna\.txt/, - /multiqc_sources\.txt/, - /multiqc_star\.txt/, - /picard_deduplication-(cnt|pct)\.(pdf|png|svg)/, - /picard_deduplication\.txt/, - /qualimap_gene_coverage_profile_Counts\.(pdf|svg)/, - /qualimap_gene_coverage_profile_Normalised\.(pdf|svg)/, - /qualimap_genomic_origin-(cnt|pct)\.(pdf|png|svg)/, - /qualimap_genomic_origin\.txt/, - /qualimap_rnaseq_genome_results\.txt/, - /rsem_assignment_plot\.txt/, - /rsem_assignment_plot-(cnt|pct)\.(pdf|png|svg)/, - /rsem_multimapping_rates\.(pdf|svg|txt)/, - /rseqc_bam_stat\.(pdf|png|svg|txt)/, - /rseqc_infer_experiment_plot\.(pdf|svg)/, - /rseqc_inner_.*/, - /rseqc_junction_.*/, - /rseqc_read_distribution_.*/, - /rseqc_read_dups\.txt/, - /rseqc_read_dups_plot\.(pdf|svg)/, - /rseqc_read_dups_plot\.txt/, - /(salmon|star_rsem)_deseq2_(clustering|pca)-plot\.(pdf|png|svg)/, - /(salmon|star_rsem)_deseq2_(pca|pca)-plot\.(pdf|png|svg)/, - /salmon_plot\.(pdf|png|svg|txt)/, - /samtools-flagstat.*/, - /samtools-idxstats-mapped-reads-plot_Normalised_Counts-(cnt|pct)\.(pdf|svg)/, - /samtools-idxstats-mapped-reads-plot_Normalised_Counts-log\.(pdf|svg)/, - /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-(cnt|pct)\.(pdf|svg)/, - /samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log\.(pdf|svg)/, - /samtools-idxstats-mapped-reads-plot_Raw_Counts-(cnt|pct)\.(pdf|svg)/, - /samtools-idxstats-mapped-reads-plot_Raw_Counts-log\.(pdf|svg)/, - /samtools-stats-dp\.(pdf|png|svg|txt)/, - /(samtools|star)_alignment_plot.*/, - /sortmerna-detailed-plot-(cnt|pct)\.(pdf|svg)/, - /sortmerna-detailed-plot\.txt/, - /(star_rsem|star_salmon)_deseq2_(clustering|pca)-plot(.*)?\.(pdf|png|svg)/, - /star_summary_table\.(pdf|png|svg|txt)/, - - // To exclude from deseq2_qc - /RAP1_IAA_30M_REP1\.txt/, - /RAP1_UNINDUCED_REP1\.txt/, - /RAP1_UNINDUCED_REP2\.txt/, - /WT_REP1\.txt/, - /WT_REP2\.txt/, - /deseq2.*/, - - // To exclude from kallisto - /abundance\.(h5|tsv)/, - /kallisto_quant\.log/, - /run_info\.json/, - - // To exclude from salmon quant - /fld\.gz/, - /meta_info\.json/, - /flenDist\.txt/, - /salmon_quant\.log/, - /quant\.genes\.sf/, - /quant\.sf/, - - // To exclude from kallisto|salmon aligners - /(kallisto|salmon)\.merged.*/, - - // To exclude from star_rsem - /.*.(genes|isoforms)\.results/, - /.*.(cnt|model|theta)/, - - // To exclude bigwig - /.*\.(forward|reverse)\.bigWig/, - - // To exclude dupradar - /.*_(duprateExpBoxplot|duprateExpDens|expressionHist)\.(pdf|png|svg)/, - - // To exclude featurecounts - /.*\.featureCounts\.txt\.summary/, - - // To exclude star salmon - /.*\.Log\.?(final|progress)?\.out/, - - // To exclude Picard Markduplicates metrics - /.*\.markdup\.sorted\.MarkDuplicates\.metrics\.txt/, - - // To exclude Qualimap files - /Junction\sAnalysis\.png/, - /Reads\sGenomic\sOrigin\.png/, - /qualimapReport\.html/, - /rnaseq_qc_results\.txt/, - - // To exclude rseqc - /.*\.DupRate_plot\.(pdf|r)/, - /.*\.inner_distance.*/, - /.*\.junction.*/, - /.*\.(pos|seq)\.DupRate\.xls/, - /.*\.read_distribution\.txt/, - /.*\.splice_(events|junction)\.(pdf|png|svg)/, - /.*\.bam_stat\.txt/, - - // To exclude from samtools stats - /.*\.sorted\.bam\.(flagstat|idxstats|stats)/, - - // To exclude from hisat2 - /.*hisat2\.summary/, - - // To exclude from stringtie - /t_data\.ctab/, - /.*\.coverage\.gtf/, - /.*\.gene\.abundance\.txt/, - /.*\.transcripts\.gtf/, - - // To exclude from sortmerna - /.*\.sortmerna\.log/, - - // To exclude log from star rsem - /RAP1_IAA_30M_REP1\.log/, - /RAP1_UNINDUCED_REP1\.log/, - /RAP1_UNINDUCED_REP2\.log/, - /WT_REP1\.log/, - /WT_REP2\.log/, - - // To exclude markdup - /.*\.markdup\.sorted\.bam(\.bai)?/, - - // To exclude trimgalore - /.*\.fastq\.gz_trimming_report\.txt/ - ] -} diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index f05b94796..04a65c99a 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -14,16 +14,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents @@ -46,16 +46,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index 14a65e9eb..7d269c5bf 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -14,16 +14,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents @@ -46,16 +46,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index a30fa248c..01d7a27fe 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -16,16 +16,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents @@ -50,16 +50,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index e996e8d4c..74e09f92d 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -14,16 +14,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents @@ -46,16 +46,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index 4dc4cb54e..b7600628f 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -14,16 +14,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 6beb1804d..6e5e60425 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -14,16 +14,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents @@ -46,16 +46,16 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = UTILS.getAllFilesFromDir(params.outdir, true, UTILS.exclusionRegexesForUnstableFileNames) + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = UTILS.getAllFilesFromDir(params.outdir, false, UTILS.exclusionRegexesForUnstableFileNames + UTILS_PIPELINE.exclusionRegexesForUnstableFileContents) + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name stable_name*.name, // All files with stable contents From 07ba1b9a2e54ca4e89a6b6f2682c9572319306f7 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 1 Oct 2024 11:12:29 +0200 Subject: [PATCH 091/100] update nftignore --- tests/.nftignore | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 2328576b7..7e7d51cd5 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,10 +1,15 @@ **/*DupRate_plot.{pdf,r} +**/*Log.out **/*Log.{final,progress}.out +**/*_fastqc.{html,zip} +**/*_raw.{html,zip} +**/*_{duprateExpBoxplot,duprateExpDens,expressionHist}.{pdf,png,svg} **/*bam_stat.txt **/*coverage.gtf **/*fastq.gz_trimming_report.txt **/*featureCounts.txt.summary **/*gene.abundance.txt +**/*hisat2.summary **/*inner_distance* **/*junction* **/*markdup.sorted.MarkDuplicates.metrics.txt @@ -13,25 +18,21 @@ **/*sorted.bam.{flagstat,idxstats,stats} **/*sortmerna.log **/*splice_{events,junction}.{pdf,png,svg} -**/*stats.txt **/*transcripts.gtf **/*{cnt,model,theta} **/*{css,gif,js} **/*{forward,reverse}.bigWig **/*{genes,isoforms}.results **/*{pos,seq}.DupRate.xls -**/*_fastqc.{html,zip} -**/*_raw.{html,zip} -**/*_{duprateExpBoxplot,duprateExpDens,expressionHist}.{pdf,png,svg} -**/*hisat2.summary -**/Junction\sAnalysis.png +**/*{salmon,star_salmon,star_rsem}_deseq2_clustering-plot*{pdf,png,txt} +**/Junction*.png **/RAP1_IAA_30M_REP1.log **/RAP1_IAA_30M_REP1.txt **/RAP1_UNINDUCED_REP1.log **/RAP1_UNINDUCED_REP1.txt **/RAP1_UNINDUCED_REP2.log **/RAP1_UNINDUCED_REP2.txt -**/Reads\sGenomic\sOrigin.png +**/Reads*.png **/WT_REP1.log **/WT_REP1.txt **/WT_REP2.log @@ -124,8 +125,8 @@ **/star_summary_table.{pdf,png,svg,txt} **/t_data.ctab **/{kallisto,salmon}.merged* -**/*{salmon,star_salmon,star_rsem}_deseq2_clustering-plot*{pdf,png,txt} **/{salmon,star_rsem}_deseq2_{clustering,pca}-plot.{pdf,png,svg} **/{salmon,star_rsem}_deseq2_{pca,pca}-plot.{pdf,png,svg} **/{samtools,star}_alignment_plot* **/{star_rsem,star_salmon}_deseq2_{clustering,pca}-plot*{pdf,png,svg} +pipeline_info/*.{html,json,txt,yml} From a83ce562aabe42ae25a95c3d7152618995e4620c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 1 Oct 2024 11:13:09 +0200 Subject: [PATCH 092/100] update pipeline versions in snapshot --- tests/default.nf.test.snap | 4 ++-- tests/featurecounts_group_type.nf.test.snap | 4 ++-- tests/hisat2.nf.test.snap | 4 ++-- tests/kallisto.nf.test.snap | 4 ++-- tests/min_mapped_reads.nf.test.snap | 4 ++-- tests/remove_ribo_rna.nf.test.snap | 4 ++-- tests/salmon.nf.test.snap | 4 ++-- tests/skip_qc.nf.test.snap | 4 ++-- tests/skip_trimming.nf.test.snap | 2 +- tests/star_rsem.nf.test.snap | 4 ++-- 10 files changed, 19 insertions(+), 19 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index e262b5263..539c03293 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -43,7 +43,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ @@ -227,7 +227,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 6b66ed182..20ef22bf7 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -43,7 +43,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ @@ -221,7 +221,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index e22c96e5c..083c40e73 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -44,7 +44,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ @@ -224,7 +224,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 1cf20c754..309685f77 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -56,7 +56,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ @@ -305,7 +305,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 1323e1090..59bce6979 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -134,7 +134,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ @@ -1321,7 +1321,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 6e506b035..d04e925ad 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -140,7 +140,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ @@ -1571,7 +1571,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 6ec67755a..cd282b8f5 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -50,7 +50,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ @@ -378,7 +378,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 316818792..f61ecd69e 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -40,7 +40,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ @@ -169,7 +169,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 8591548f9..2f7288589 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -130,7 +130,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index c9881f337..34c02700e 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -134,7 +134,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ @@ -1450,7 +1450,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.0dev" + "nf-core/rnaseq": "v3.15.2" } }, [ From b80c6c58c82c28cde3d9a4c0150ee1706943eb94 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 1 Oct 2024 12:09:55 +0200 Subject: [PATCH 093/100] update CHANGELOG --- CHANGELOG.md | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a87075994..8a43259a0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [[3.15.2](https://github.com/nf-core/rnaseq/releases/tag/3.15.2)] - 2024-10-01 +### Credits + +Special thanks to the following for their contributions to the release: + +- [Adam Talbot](https://github.com/adamrtalbot) +- [Ezra Greenberg](https://github.com/egreenberg7) +- [Jonathan Manning](https://github.com/pinin4fjords) +- [Matthias Zepper](https://github.com/MatthiasZepper) +- [Maxime Garcia](https://github.com/maxulysse) +- [Paolo Di Tommaso](https://github.com/pditommaso) +- [Phil Ewels](https://github.com/ewels) +- [Shaun Regenbaum](https://github.com/Shaun-Regenbaum) + ### Enhancements & fixes - [PR #1376](https://github.com/nf-core/rnaseq/pull/1376) - Fix invalid named parameter syntax @@ -40,19 +53,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 > > **NB:** Dependency has been **removed** if new version information isn't present. -### Credits - -Special thanks to the following for their contributions to the release: - -- [Adam Talbot](https://github.com/adamrtalbot) -- [Ezra Greenberg](https://github.com/egreenberg7) -- [Jonathan Manning](https://github.com/pinin4fjords) -- [Matthias Zepper](https://github.com/MatthiasZepper) -- [Maxime Garcia](https://github.com/maxulysse) -- [Paolo Di Tommaso](https://github.com/pditommaso) -- [Phil Ewels](https://github.com/ewels) -- [Shaun Regenbaum](https://github.com/Shaun-Regenbaum) - ## [[3.15.1](https://github.com/nf-core/rnaseq/releases/tag/3.15.1)] - 2024-09-16 ### Enhancements & fixes From 7d14c7431b716e2f8cf7ace49fe01199a0c912ff Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 1 Oct 2024 12:13:45 +0200 Subject: [PATCH 094/100] update nftignore --- tests/.nftignore | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 7e7d51cd5..ced58fbb8 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -26,17 +26,7 @@ **/*{pos,seq}.DupRate.xls **/*{salmon,star_salmon,star_rsem}_deseq2_clustering-plot*{pdf,png,txt} **/Junction*.png -**/RAP1_IAA_30M_REP1.log -**/RAP1_IAA_30M_REP1.txt -**/RAP1_UNINDUCED_REP1.log -**/RAP1_UNINDUCED_REP1.txt -**/RAP1_UNINDUCED_REP2.log -**/RAP1_UNINDUCED_REP2.txt **/Reads*.png -**/WT_REP1.log -**/WT_REP1.txt -**/WT_REP2.log -**/WT_REP2.txt **/abundance.{h5,tsv} **/cutadapt_filtered_reads_plot-{cnt,pct}.{pdf,svg} **/cutadapt_trimmed_sequences_*{pdf,svg} @@ -129,4 +119,7 @@ **/{salmon,star_rsem}_deseq2_{pca,pca}-plot.{pdf,png,svg} **/{samtools,star}_alignment_plot* **/{star_rsem,star_salmon}_deseq2_{clustering,pca}-plot*{pdf,png,svg} +bbsplit/*.stats.txt pipeline_info/*.{html,json,txt,yml} +salmon/deseq2_qc/size_factors/*.txt +star_rsem/log/*.log From 2b856b76ae56b09cabe7629028a28464117c1f65 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 1 Oct 2024 13:40:00 +0200 Subject: [PATCH 095/100] update nftignore --- tests/.nftignore | 2 +- tests/default.nf.test.snap | 4 ++-- tests/featurecounts_group_type.nf.test.snap | 4 ++-- tests/hisat2.nf.test.snap | 4 ++-- tests/kallisto.nf.test.snap | 4 ++-- tests/min_mapped_reads.nf.test.snap | 4 ++-- tests/remove_ribo_rna.nf.test.snap | 4 ++-- tests/salmon.nf.test.snap | 4 ++-- tests/skip_qc.nf.test.snap | 4 ++-- tests/skip_trimming.nf.test.snap | 2 +- tests/star_rsem.nf.test.snap | 4 ++-- 11 files changed, 20 insertions(+), 20 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index ced58fbb8..dcbd8d8a8 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -121,5 +121,5 @@ **/{star_rsem,star_salmon}_deseq2_{clustering,pca}-plot*{pdf,png,svg} bbsplit/*.stats.txt pipeline_info/*.{html,json,txt,yml} -salmon/deseq2_qc/size_factors/*.txt +**/deseq2_qc/size_factors/*.txt star_rsem/log/*.log diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 539c03293..e262b5263 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -43,7 +43,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -227,7 +227,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 20ef22bf7..6b66ed182 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -43,7 +43,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -221,7 +221,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 083c40e73..e22c96e5c 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -44,7 +44,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -224,7 +224,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 309685f77..1cf20c754 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -56,7 +56,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -305,7 +305,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 59bce6979..1323e1090 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -134,7 +134,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -1321,7 +1321,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index d04e925ad..6e506b035 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -140,7 +140,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -1571,7 +1571,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index cd282b8f5..6ec67755a 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -50,7 +50,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -378,7 +378,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index f61ecd69e..316818792 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -40,7 +40,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -169,7 +169,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 2f7288589..8591548f9 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -130,7 +130,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 34c02700e..c9881f337 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -134,7 +134,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ @@ -1450,7 +1450,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.15.2" + "nf-core/rnaseq": "v3.16.0dev" } }, [ From 1d50d3166125c01cbe2be3f7b135bfc1fd24bd70 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 1 Oct 2024 13:47:23 +0200 Subject: [PATCH 096/100] 3.16.0 instead of 3.15.2 --- nextflow.config | 2 +- tests/default.nf.test.snap | 4 ++-- tests/featurecounts_group_type.nf.test.snap | 4 ++-- tests/hisat2.nf.test.snap | 4 ++-- tests/kallisto.nf.test.snap | 10 +++++----- tests/min_mapped_reads.nf.test.snap | 4 ++-- tests/remove_ribo_rna.nf.test.snap | 4 ++-- tests/salmon.nf.test.snap | 4 ++-- tests/skip_qc.nf.test.snap | 4 ++-- tests/skip_trimming.nf.test.snap | 2 +- tests/star_rsem.nf.test.snap | 4 ++-- workflows/rnaseq/assets/multiqc/multiqc_config.yml | 2 +- 12 files changed, 24 insertions(+), 24 deletions(-) diff --git a/nextflow.config b/nextflow.config index 6d58c9224..d2b1f40a9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -345,7 +345,7 @@ manifest { description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '3.15.2' + version = '3.16.0' doi = 'https://doi.org/10.5281/zenodo.1400710' } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 78107dc37..4fb30e3c9 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -266,7 +266,7 @@ }, "Params: default - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -932,7 +932,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 13c036a1c..0ff2673a8 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -747,7 +747,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}" ], "meta": { "nf-test": "0.9.0", @@ -757,7 +757,7 @@ }, "Params: --featurecounts_group_type false - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 3c7e95bb3..e4d0442db 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -631,7 +631,7 @@ }, "Params: --aligner hisat2 - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -726,7 +726,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_ALIGN={hisat2=2.2.1, samtools=1.16.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_ALIGN={hisat2=2.2.1, samtools=1.16.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 775cb1689..a816ac41b 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -99,11 +99,11 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:25:12.683541" + "timestamp": "2024-08-23.16.05:12.683541" }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, KALLISTO_QUANT={kallisto=0.48.0}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, KALLISTO_QUANT={kallisto=0.48.0}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}" ], "meta": { "nf-test": "0.9.0", @@ -134,7 +134,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:25:12.695474" + "timestamp": "2024-08-23.16.05:12.695474" }, "multiqc_plots": { "content": [ @@ -215,11 +215,11 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:25:12.672876" + "timestamp": "2024-08-23.16.05:12.672876" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "multiqc_report.html", diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index d80815389..fa7f6e03a 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -447,7 +447,7 @@ }, "Params: --min_mapped_reads 90 - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -854,7 +854,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 4f0e59c1c..5f3c58a55 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -498,7 +498,7 @@ }, "Params: --remove_ribo_rna - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -954,7 +954,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, SORTMERNA={sortmerna=4.3.6}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, SORTMERNA={sortmerna=4.3.6}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index e4d4fd48c..0b68666ee 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -61,7 +61,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}" ], "meta": { "nf-test": "0.9.0", @@ -265,7 +265,7 @@ }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 7cba6b400..8d5a202c3 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -157,7 +157,7 @@ }, "Params: --skip_qc - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -477,7 +477,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index dff48a776..641141442 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -751,7 +751,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 9377ad70d..dd4e2b0be 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -766,7 +766,7 @@ }, "Params: --aligner star_rsem - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -797,7 +797,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_RSEM={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEM_CALCULATEEXPRESSION={rsem=1.3.1, star=2.7.10a}, RSEM_MERGE_COUNTS={sed=4.7}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.2}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_RSEM={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEM_CALCULATEEXPRESSION={rsem=1.3.1, star=2.7.10a}, RSEM_MERGE_COUNTS={sed=4.7}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0}}" ], "meta": { "nf-test": "0.9.0", diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml index b8dbc608d..dd8bc621c 100644 --- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml +++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation. + This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: # Important checks and failures sample-status: From d19cea4fa7fc75cc9055e8ef5ae0078599d13833 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 1 Oct 2024 15:56:24 +0200 Subject: [PATCH 097/100] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8a43259a0..4ad220327 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [[3.15.2](https://github.com/nf-core/rnaseq/releases/tag/3.15.2)] - 2024-10-01 +## [[3.16.0](https://github.com/nf-core/rnaseq/releases/tag/3.16.0)] - 2024-10-02 ### Credits From 1d35e2a1e00e48fd3e7dfedf5f9bfec93087cd12 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 2 Oct 2024 08:41:08 +0200 Subject: [PATCH 098/100] use nft-utils 0.0.2 to get relative path in snapshots --- nf-test.config | 2 +- tests/default.nf.test | 8 +- tests/default.nf.test.snap | 2178 +++++++++--------- tests/featurecounts_group_type.nf.test | 8 +- tests/featurecounts_group_type.nf.test.snap | 2120 +++++++++--------- tests/hisat2.nf.test | 8 +- tests/hisat2.nf.test.snap | 1926 ++++++++-------- tests/kallisto.nf.test | 8 +- tests/kallisto.nf.test.snap | 352 +-- tests/min_mapped_reads.nf.test | 8 +- tests/min_mapped_reads.nf.test.snap | 1844 ++++++++-------- tests/remove_ribo_rna.nf.test | 8 +- tests/remove_ribo_rna.nf.test.snap | 2204 +++++++++---------- tests/salmon.nf.test | 8 +- tests/salmon.nf.test.snap | 456 ++-- tests/skip_qc.nf.test | 8 +- tests/skip_qc.nf.test.snap | 1018 ++++----- tests/skip_trimming.nf.test | 4 +- tests/skip_trimming.nf.test.snap | 1940 ++++++++-------- tests/star_rsem.nf.test | 8 +- tests/star_rsem.nf.test.snap | 2038 ++++++++--------- 21 files changed, 8077 insertions(+), 8077 deletions(-) diff --git a/nf-test.config b/nf-test.config index 2f04d4302..c843dabec 100644 --- a/nf-test.config +++ b/nf-test.config @@ -13,6 +13,6 @@ config { // load the necessary plugins plugins { load "nft-bam@0.3.0" - load "nft-utils@0.0.1" + load "nft-utils@0.0.2" } } diff --git a/tests/default.nf.test b/tests/default.nf.test index 1e5c84d4b..80b19646a 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -23,8 +23,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -54,8 +54,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index e262b5263..13dccd5f5 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -48,38 +48,38 @@ }, [ "custom", - "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", "fastqc", - "raw", - "RAP1_IAA_30M_REP1_raw.html", - "RAP1_IAA_30M_REP1_raw.zip", - "RAP1_UNINDUCED_REP1_raw.html", - "RAP1_UNINDUCED_REP1_raw.zip", - 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"star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls", + "star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls", + "star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls", + "star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls", + "star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls", + "star_salmon/rseqc/junction_saturation", + "star_salmon/rseqc/junction_saturation/pdf", + "star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf", + "star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf", + "star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf", + "star_salmon/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf", + "star_salmon/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf", + "star_salmon/rseqc/junction_saturation/rscript", + "star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r", + "star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r", + "star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r", + "star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r", + "star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r", + "star_salmon/rseqc/read_distribution", + "star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt", + "star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt", + "star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt", + "star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt", + "star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt", + "star_salmon/rseqc/read_duplication", + "star_salmon/rseqc/read_duplication/pdf", + "star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/rscript", + "star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls", + "star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts.tsv", + "star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts_length_scaled.tsv", + "star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts_scaled.tsv", + "star_salmon/salmon.merged.gene_lengths.tsv", + "star_salmon/salmon.merged.gene_tpm.tsv", + "star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds", + "star_salmon/salmon.merged.transcript_counts.tsv", + "star_salmon/salmon.merged.transcript_lengths.tsv", + "star_salmon/salmon.merged.transcript_tpm.tsv", + "star_salmon/samtools_stats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.stats", + "star_salmon/stringtie", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf", + "star_salmon/stringtie/WT_REP1.ballgown", + "star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/WT_REP1.coverage.gtf", + "star_salmon/stringtie/WT_REP1.gene.abundance.txt", + "star_salmon/stringtie/WT_REP1.transcripts.gtf", + "star_salmon/stringtie/WT_REP2.ballgown", + "star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/WT_REP2.coverage.gtf", + "star_salmon/stringtie/WT_REP2.gene.abundance.txt", + "star_salmon/stringtie/WT_REP2.transcripts.gtf", + "star_salmon/tx2gene.tsv", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -1591,8 +1591,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.08.0" }, - "timestamp": "2024-09-19T18:59:10.651567" + "timestamp": "2024-10-02T08:39:09.000328" } } \ No newline at end of file diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index a05949f84..fcd11c1da 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 6b66ed182..a74557fc7 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -48,38 +48,38 @@ }, [ "custom", - "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", "fastqc", - "raw", - "RAP1_IAA_30M_REP1_raw.html", - "RAP1_IAA_30M_REP1_raw.zip", - "RAP1_UNINDUCED_REP1_raw.html", - "RAP1_UNINDUCED_REP1_raw.zip", - "RAP1_UNINDUCED_REP2_raw.html", - "RAP1_UNINDUCED_REP2_raw.zip", - "WT_REP1_raw.html", - "WT_REP1_raw.zip", - "WT_REP2_raw.html", - "WT_REP2_raw.zip", - "trim", + "fastqc/raw", + "fastqc/raw/RAP1_IAA_30M_REP1_raw.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw.zip", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw.html", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw.html", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip", + "fastqc/raw/WT_REP1_raw.html", + "fastqc/raw/WT_REP1_raw.zip", + "fastqc/raw/WT_REP2_raw.html", + "fastqc/raw/WT_REP2_raw.zip", + "fastqc/trim", "multiqc", - "star_salmon", - "multiqc_data", - "multiqc_plots", - "multiqc_report.html", + "multiqc/star_salmon", + "multiqc/star_salmon/multiqc_data", + "multiqc/star_salmon/multiqc_plots", + "multiqc/star_salmon/multiqc_report.html", "pipeline_info", - "nf_core_rnaseq_software_mqc_versions.yml", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - 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"star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf", + "star_salmon/stringtie/WT_REP1.ballgown", + "star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/WT_REP1.coverage.gtf", + "star_salmon/stringtie/WT_REP1.gene.abundance.txt", + "star_salmon/stringtie/WT_REP1.transcripts.gtf", + "star_salmon/stringtie/WT_REP2.ballgown", + "star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/WT_REP2.coverage.gtf", + "star_salmon/stringtie/WT_REP2.gene.abundance.txt", + "star_salmon/stringtie/WT_REP2.transcripts.gtf", + "star_salmon/tx2gene.tsv", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -1541,6 +1541,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:07:14.922532" + "timestamp": "2024-10-02T07:37:24.538529" } } \ No newline at end of file diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index ff9e4d99d..e743a37d4 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index e22c96e5c..99ddfa937 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -49,38 +49,38 @@ }, [ "custom", - "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", "fastqc", - "raw", - "RAP1_IAA_30M_REP1_raw.html", - "RAP1_IAA_30M_REP1_raw.zip", - "RAP1_UNINDUCED_REP1_raw.html", - "RAP1_UNINDUCED_REP1_raw.zip", - "RAP1_UNINDUCED_REP2_raw.html", - "RAP1_UNINDUCED_REP2_raw.zip", - "WT_REP1_raw.html", - "WT_REP1_raw.zip", - "WT_REP2_raw.html", - "WT_REP2_raw.zip", - "trim", + "fastqc/raw", + "fastqc/raw/RAP1_IAA_30M_REP1_raw.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw.zip", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw.html", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw.html", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip", + "fastqc/raw/WT_REP1_raw.html", + "fastqc/raw/WT_REP1_raw.zip", + "fastqc/raw/WT_REP2_raw.html", + "fastqc/raw/WT_REP2_raw.zip", + "fastqc/trim", "multiqc", - "hisat2", - "multiqc_data", - "multiqc_plots", - "multiqc_report.html", + "multiqc/hisat2", + "multiqc/hisat2/multiqc_data", + "multiqc/hisat2/multiqc_plots", + "multiqc/hisat2/multiqc_report.html", "pipeline_info", - "nf_core_rnaseq_software_mqc_versions.yml", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -91,7 +91,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:13:54.347768" + "timestamp": "2024-10-02T07:43:50.371605" }, "Params: --aligner hisat2": { "content": [ @@ -229,946 +229,946 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt", + "bbsplit/RAP1_IAA_30M_REP1.stats.txt", + 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"hisat2/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt", + "hisat2/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt", + "hisat2/rseqc/junction_annotation", + "hisat2/rseqc/junction_annotation/bed", + "hisat2/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed", + "hisat2/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed", + "hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed", + "hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed", + "hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed", + "hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed", + "hisat2/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed", + "hisat2/rseqc/junction_annotation/bed/WT_REP1.junction.bed", + "hisat2/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed", + "hisat2/rseqc/junction_annotation/bed/WT_REP2.junction.bed", + "hisat2/rseqc/junction_annotation/log", + "hisat2/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log", + "hisat2/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log", + "hisat2/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log", + "hisat2/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log", + "hisat2/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log", + "hisat2/rseqc/junction_annotation/pdf", + "hisat2/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf", + "hisat2/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf", + "hisat2/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf", + "hisat2/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf", + "hisat2/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf", + "hisat2/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf", + "hisat2/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf", + 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"salmon/RAP1_IAA_30M_REP1/aux_info", + "salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv", + "salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz", + "salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz", + "salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json", + "salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz", + "salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz", + "salmon/RAP1_IAA_30M_REP1/cmd_info.json", + "salmon/RAP1_IAA_30M_REP1/libParams", + "salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt", + "salmon/RAP1_IAA_30M_REP1/lib_format_counts.json", + "salmon/RAP1_IAA_30M_REP1/logs", + "salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log", + "salmon/RAP1_IAA_30M_REP1/quant.genes.sf", + "salmon/RAP1_IAA_30M_REP1/quant.sf", + "salmon/RAP1_UNINDUCED_REP1", + "salmon/RAP1_UNINDUCED_REP1/aux_info", + "salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv", + "salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz", + "salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz", + "salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json", + "salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz", + "salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz", + "salmon/RAP1_UNINDUCED_REP1/cmd_info.json", + "salmon/RAP1_UNINDUCED_REP1/libParams", + "salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt", + "salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json", + "salmon/RAP1_UNINDUCED_REP1/logs", + "salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log", + "salmon/RAP1_UNINDUCED_REP1/quant.genes.sf", + "salmon/RAP1_UNINDUCED_REP1/quant.sf", + "salmon/RAP1_UNINDUCED_REP2", + "salmon/RAP1_UNINDUCED_REP2/aux_info", + "salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv", + "salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz", + "salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz", + "salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json", + "salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz", + "salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz", + "salmon/RAP1_UNINDUCED_REP2/cmd_info.json", + "salmon/RAP1_UNINDUCED_REP2/libParams", + "salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt", + "salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json", + "salmon/RAP1_UNINDUCED_REP2/logs", + "salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log", + "salmon/RAP1_UNINDUCED_REP2/quant.genes.sf", + "salmon/RAP1_UNINDUCED_REP2/quant.sf", + "salmon/WT_REP1", + "salmon/WT_REP1/aux_info", + "salmon/WT_REP1/aux_info/ambig_info.tsv", + "salmon/WT_REP1/aux_info/expected_bias.gz", + "salmon/WT_REP1/aux_info/fld.gz", + "salmon/WT_REP1/aux_info/meta_info.json", + "salmon/WT_REP1/aux_info/observed_bias.gz", + "salmon/WT_REP1/aux_info/observed_bias_3p.gz", + "salmon/WT_REP1/cmd_info.json", + "salmon/WT_REP1/libParams", + "salmon/WT_REP1/libParams/flenDist.txt", + "salmon/WT_REP1/lib_format_counts.json", + "salmon/WT_REP1/logs", + "salmon/WT_REP1/logs/salmon_quant.log", + "salmon/WT_REP1/quant.genes.sf", + "salmon/WT_REP1/quant.sf", + "salmon/WT_REP2", + "salmon/WT_REP2/aux_info", + "salmon/WT_REP2/aux_info/ambig_info.tsv", + "salmon/WT_REP2/aux_info/expected_bias.gz", + "salmon/WT_REP2/aux_info/fld.gz", + "salmon/WT_REP2/aux_info/meta_info.json", + "salmon/WT_REP2/aux_info/observed_bias.gz", + "salmon/WT_REP2/aux_info/observed_bias_3p.gz", + "salmon/WT_REP2/cmd_info.json", + "salmon/WT_REP2/libParams", + "salmon/WT_REP2/libParams/flenDist.txt", + "salmon/WT_REP2/lib_format_counts.json", + "salmon/WT_REP2/logs", + "salmon/WT_REP2/logs/salmon_quant.log", + "salmon/WT_REP2/quant.genes.sf", + "salmon/WT_REP2/quant.sf", + "salmon/deseq2_qc", + "salmon/deseq2_qc/R_sessionInfo.log", + "salmon/deseq2_qc/deseq2.dds.RData", + "salmon/deseq2_qc/deseq2.pca.vals.txt", + "salmon/deseq2_qc/deseq2.plots.pdf", + "salmon/deseq2_qc/deseq2.sample.dists.txt", + "salmon/deseq2_qc/size_factors", + "salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt", + "salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt", + "salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt", + "salmon/deseq2_qc/size_factors/WT_REP1.txt", + "salmon/deseq2_qc/size_factors/WT_REP2.txt", + "salmon/deseq2_qc/size_factors/deseq2.size_factors.RData", + "salmon/salmon.merged.gene_counts.SummarizedExperiment.rds", + "salmon/salmon.merged.gene_counts.tsv", + "salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds", + "salmon/salmon.merged.gene_counts_length_scaled.tsv", + "salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds", + "salmon/salmon.merged.gene_counts_scaled.tsv", + "salmon/salmon.merged.gene_lengths.tsv", + "salmon/salmon.merged.gene_tpm.tsv", + "salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds", + "salmon/salmon.merged.transcript_counts.tsv", + "salmon/salmon.merged.transcript_lengths.tsv", + "salmon/salmon.merged.transcript_tpm.tsv", + "salmon/tx2gene.tsv", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -1439,6 +1439,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:13:07.804677" + "timestamp": "2024-10-02T07:43:07.13584" } } \ No newline at end of file diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index fed4532f8..0c6816a59 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -26,8 +26,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -60,8 +60,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 1cf20c754..d69ef977c 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -61,170 +61,170 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt", + "bbsplit/RAP1_IAA_30M_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP2.stats.txt", + "bbsplit/WT_REP1.stats.txt", + "bbsplit/WT_REP2.stats.txt", "custom", - "out", - "genome_gfp.fasta", - "genome_gfp.gtf", + "custom/out", + "custom/out/genome_gfp.fasta", + 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"fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip", "kallisto", - "RAP1_IAA_30M_REP1", - "abundance.h5", - "abundance.tsv", - "kallisto_quant.log", - "run_info.json", - "RAP1_UNINDUCED_REP1", - "abundance.h5", - "abundance.tsv", - "kallisto_quant.log", - "run_info.json", - "RAP1_UNINDUCED_REP2", - "abundance.h5", 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"kallisto/RAP1_IAA_30M_REP1/kallisto_quant.log", + "kallisto/RAP1_IAA_30M_REP1/run_info.json", + "kallisto/RAP1_UNINDUCED_REP1", + "kallisto/RAP1_UNINDUCED_REP1/abundance.h5", + "kallisto/RAP1_UNINDUCED_REP1/abundance.tsv", + "kallisto/RAP1_UNINDUCED_REP1/kallisto_quant.log", + "kallisto/RAP1_UNINDUCED_REP1/run_info.json", + "kallisto/RAP1_UNINDUCED_REP2", + "kallisto/RAP1_UNINDUCED_REP2/abundance.h5", + "kallisto/RAP1_UNINDUCED_REP2/abundance.tsv", + "kallisto/RAP1_UNINDUCED_REP2/kallisto_quant.log", + "kallisto/RAP1_UNINDUCED_REP2/run_info.json", + "kallisto/WT_REP1", + "kallisto/WT_REP1/abundance.h5", + "kallisto/WT_REP1/abundance.tsv", + "kallisto/WT_REP1/kallisto_quant.log", + "kallisto/WT_REP1/run_info.json", + "kallisto/WT_REP2", + "kallisto/WT_REP2/abundance.h5", + "kallisto/WT_REP2/abundance.tsv", + "kallisto/WT_REP2/kallisto_quant.log", + "kallisto/WT_REP2/run_info.json", + "kallisto/kallisto.merged.gene_counts.SummarizedExperiment.rds", + 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"multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg", + "multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg", + "multiqc/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/multiqc_report_plots/svg/general_stats_table.svg", + "multiqc/multiqc_report_plots/svg/kallisto_alignment-cnt.svg", + "multiqc/multiqc_report_plots/svg/kallisto_alignment-pct.svg", "pipeline_info", - "nf_core_rnaseq_software_mqc_versions.yml", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -264,7 +264,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:17:00.197522" + "timestamp": "2024-10-02T07:46:44.393695" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ @@ -310,26 +310,26 @@ }, [ "custom", - "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", "fastqc", - "trim", + "fastqc/trim", "multiqc", - "multiqc_data", - "multiqc_plots", - "multiqc_report.html", + "multiqc/multiqc_data", + "multiqc/multiqc_plots", + "multiqc/multiqc_report.html", "pipeline_info", - "nf_core_rnaseq_software_mqc_versions.yml", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -340,6 +340,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:17:38.870034" + "timestamp": "2024-10-02T07:47:31.044439" } } \ No newline at end of file diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index 04a65c99a..7ffef71de 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 1323e1090..69637a301 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -139,905 +139,905 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt", + "bbsplit/RAP1_IAA_30M_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP2.stats.txt", + "bbsplit/WT_REP1.stats.txt", + "bbsplit/WT_REP2.stats.txt", "custom", - "out", - "genome_gfp.fasta", - "genome_gfp.gtf", + "custom/out", + "custom/out/genome_gfp.fasta", + 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"star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf", + "star_salmon/tx2gene.tsv", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -1275,7 +1275,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:24:21.094029" + "timestamp": "2024-10-02T07:54:27.006271" }, "Params: --min_mapped_reads 90 - stub": { "content": [ @@ -1326,38 +1326,38 @@ }, [ "custom", - "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", "fastqc", - "raw", - "RAP1_IAA_30M_REP1_raw.html", - "RAP1_IAA_30M_REP1_raw.zip", - "RAP1_UNINDUCED_REP1_raw.html", - "RAP1_UNINDUCED_REP1_raw.zip", - "RAP1_UNINDUCED_REP2_raw.html", - "RAP1_UNINDUCED_REP2_raw.zip", - "WT_REP1_raw.html", - "WT_REP1_raw.zip", - "WT_REP2_raw.html", - "WT_REP2_raw.zip", - "trim", + "fastqc/raw", + "fastqc/raw/RAP1_IAA_30M_REP1_raw.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw.zip", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw.html", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw.html", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip", + "fastqc/raw/WT_REP1_raw.html", + "fastqc/raw/WT_REP1_raw.zip", + "fastqc/raw/WT_REP2_raw.html", + "fastqc/raw/WT_REP2_raw.zip", + "fastqc/trim", "multiqc", - "star_salmon", - "multiqc_data", - "multiqc_plots", - "multiqc_report.html", + "multiqc/star_salmon", + "multiqc/star_salmon/multiqc_data", + "multiqc/star_salmon/multiqc_plots", + "multiqc/star_salmon/multiqc_report.html", "pipeline_info", - "nf_core_rnaseq_software_mqc_versions.yml", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1368,6 +1368,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:25:05.823677" + "timestamp": "2024-10-02T07:55:19.233936" } } \ No newline at end of file diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index 7d269c5bf..66084a8c9 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 6e506b035..528163582 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -145,1085 +145,1085 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt", + "bbsplit/RAP1_IAA_30M_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP2.stats.txt", + "bbsplit/WT_REP1.stats.txt", + "bbsplit/WT_REP2.stats.txt", "custom", - "out", - "genome_gfp.fasta", - "genome_gfp.gtf", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", "fastqc", - "raw", - "RAP1_IAA_30M_REP1_raw_1_fastqc.html", - "RAP1_IAA_30M_REP1_raw_1_fastqc.zip", - "RAP1_IAA_30M_REP1_raw_2_fastqc.html", - "RAP1_IAA_30M_REP1_raw_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_raw_fastqc.html", - "RAP1_UNINDUCED_REP1_raw_fastqc.zip", - "RAP1_UNINDUCED_REP2_raw_fastqc.html", - "RAP1_UNINDUCED_REP2_raw_fastqc.zip", - "WT_REP1_raw_1_fastqc.html", - "WT_REP1_raw_1_fastqc.zip", - "WT_REP1_raw_2_fastqc.html", - "WT_REP1_raw_2_fastqc.zip", - "WT_REP2_raw_1_fastqc.html", - "WT_REP2_raw_1_fastqc.zip", - "WT_REP2_raw_2_fastqc.html", - "WT_REP2_raw_2_fastqc.zip", - "trim", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", - "WT_REP1_trimmed_1_val_1_fastqc.html", - "WT_REP1_trimmed_1_val_1_fastqc.zip", - "WT_REP1_trimmed_2_val_2_fastqc.html", - "WT_REP1_trimmed_2_val_2_fastqc.zip", - "WT_REP2_trimmed_1_val_1_fastqc.html", - "WT_REP2_trimmed_1_val_1_fastqc.zip", - "WT_REP2_trimmed_2_val_2_fastqc.html", - "WT_REP2_trimmed_2_val_2_fastqc.zip", + "fastqc/raw", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip", + "fastqc/raw/WT_REP1_raw_1_fastqc.html", + "fastqc/raw/WT_REP1_raw_1_fastqc.zip", + "fastqc/raw/WT_REP1_raw_2_fastqc.html", + "fastqc/raw/WT_REP1_raw_2_fastqc.zip", + "fastqc/raw/WT_REP2_raw_1_fastqc.html", + "fastqc/raw/WT_REP2_raw_1_fastqc.zip", + "fastqc/raw/WT_REP2_raw_2_fastqc.html", + "fastqc/raw/WT_REP2_raw_2_fastqc.zip", + "fastqc/trim", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip", "multiqc", - "star_salmon", - "multiqc_report.html", - "multiqc_report_data", - "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "fastqc-status-check-heatmap-1.txt", - "fastqc-status-check-heatmap.txt", - "fastqc_adapter_content_plot.txt", - "fastqc_overrepresented_sequences_plot-1.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot-1.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot-1.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot-1.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot-1.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot-1.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", - "fastqc_top_overrepresented_sequences_table-1.txt", - "fastqc_top_overrepresented_sequences_table.txt", - "junction_saturation_known.txt", - "junction_saturation_novel.txt", - "multiqc_citations.txt", - "multiqc_cutadapt.txt", - "multiqc_data.json", - "multiqc_dupradar-section-plot.txt", - "multiqc_fail_strand_check_table.txt", - "multiqc_fastqc_fastqc_raw.txt", - "multiqc_fastqc_fastqc_trimmed.txt", - "multiqc_featurecounts_biotype_plot.txt", - "multiqc_general_stats.txt", - "multiqc_picard_dups.txt", - "multiqc_rseqc_bam_stat.txt", - "multiqc_rseqc_infer_experiment.txt", - "multiqc_rseqc_junction_annotation.txt", - "multiqc_rseqc_read_distribution.txt", - "multiqc_salmon.txt", - "multiqc_salmon_deseq2_clustering-plot.txt", - "multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc_salmon_deseq2_clustering-plot_4.txt", - "multiqc_salmon_deseq2_pca-plot.txt", - "multiqc_samtools_flagstat.txt", - "multiqc_samtools_idxstats.txt", - "multiqc_samtools_stats.txt", - "multiqc_software_versions.txt", - "multiqc_sortmerna.txt", - "multiqc_sources.txt", - "multiqc_star.txt", - "multiqc_star_salmon_deseq2_clustering-plot.txt", - "multiqc_star_salmon_deseq2_clustering-plot_1.txt", - 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"RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -1522,7 +1522,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:36:38.346296" + "timestamp": 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"fastqc/raw/WT_REP2_raw.zip", + "fastqc/trim", "multiqc", - "star_salmon", - "multiqc_data", - "multiqc_plots", - "multiqc_report.html", + "multiqc/star_salmon", + "multiqc/star_salmon/multiqc_data", + "multiqc/star_salmon/multiqc_plots", + "multiqc/star_salmon/multiqc_report.html", "pipeline_info", - "nf_core_rnaseq_software_mqc_versions.yml", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1618,6 +1618,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:37:24.981917" + "timestamp": "2024-10-02T08:08:00.752563" } -} +} \ No newline at end of file diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index 01d7a27fe..c0a386da0 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -26,8 +26,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -60,8 +60,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 6ec67755a..a66fb0068 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -55,222 +55,222 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt", + "bbsplit/RAP1_IAA_30M_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP2.stats.txt", + "bbsplit/WT_REP1.stats.txt", + "bbsplit/WT_REP2.stats.txt", "custom", - "out", - "genome_gfp.fasta", - "genome_gfp.gtf", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", "fastqc", - "trim", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", - "WT_REP1_trimmed_1_val_1_fastqc.html", - "WT_REP1_trimmed_1_val_1_fastqc.zip", - "WT_REP1_trimmed_2_val_2_fastqc.html", - "WT_REP1_trimmed_2_val_2_fastqc.zip", - "WT_REP2_trimmed_1_val_1_fastqc.html", - "WT_REP2_trimmed_1_val_1_fastqc.zip", - "WT_REP2_trimmed_2_val_2_fastqc.html", - "WT_REP2_trimmed_2_val_2_fastqc.zip", + "fastqc/trim", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip", "multiqc", - "multiqc_report.html", - "multiqc_report_data", - "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "fastqc-status-check-heatmap.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", - "fastqc_top_overrepresented_sequences_table.txt", - "multiqc_citations.txt", - "multiqc_cutadapt.txt", - "multiqc_data.json", - "multiqc_fastqc_fastqc_trimmed.txt", - "multiqc_general_stats.txt", - "multiqc_salmon.txt", - "multiqc_software_versions.txt", - "multiqc_sources.txt", - "salmon_plot.txt", - "multiqc_report_plots", - "pdf", - "cutadapt_filtered_reads_plot-cnt.pdf", - "cutadapt_filtered_reads_plot-pct.pdf", - "cutadapt_trimmed_sequences_plot_3_Counts.pdf", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "fastqc-status-check-heatmap.pdf", - "fastqc_overrepresented_sequences_plot.pdf", - "fastqc_per_base_n_content_plot.pdf", - "fastqc_per_base_sequence_quality_plot.pdf", - "fastqc_per_sequence_gc_content_plot_Counts.pdf", - "fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "fastqc_per_sequence_quality_scores_plot.pdf", - "fastqc_sequence_counts_plot-cnt.pdf", - "fastqc_sequence_counts_plot-pct.pdf", - "fastqc_sequence_duplication_levels_plot.pdf", - "fastqc_sequence_length_distribution_plot.pdf", - "fastqc_top_overrepresented_sequences_table.pdf", - "general_stats_table.pdf", - "salmon_plot.pdf", - "png", - "cutadapt_filtered_reads_plot-cnt.png", - "cutadapt_filtered_reads_plot-pct.png", - "cutadapt_trimmed_sequences_plot_3_Counts.png", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "fastqc-status-check-heatmap.png", - "fastqc_overrepresented_sequences_plot.png", - "fastqc_per_base_n_content_plot.png", - "fastqc_per_base_sequence_quality_plot.png", - "fastqc_per_sequence_gc_content_plot_Counts.png", - "fastqc_per_sequence_gc_content_plot_Percentages.png", - "fastqc_per_sequence_quality_scores_plot.png", - "fastqc_sequence_counts_plot-cnt.png", - "fastqc_sequence_counts_plot-pct.png", - "fastqc_sequence_duplication_levels_plot.png", - "fastqc_sequence_length_distribution_plot.png", - "fastqc_top_overrepresented_sequences_table.png", - "general_stats_table.png", - 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"flenDist.txt", - "lib_format_counts.json", - "logs", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "WT_REP1", - "aux_info", - "ambig_info.tsv", - "expected_bias.gz", - "fld.gz", - "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", - "libParams", - "flenDist.txt", - "lib_format_counts.json", - "logs", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "WT_REP2", - "aux_info", - "ambig_info.tsv", - "expected_bias.gz", - "fld.gz", - "meta_info.json", - "observed_bias.gz", - "observed_bias_3p.gz", - "cmd_info.json", - "libParams", - "flenDist.txt", - "lib_format_counts.json", - "logs", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "salmon.merged.gene_counts.SummarizedExperiment.rds", - "salmon.merged.gene_counts.tsv", - "salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds", - "salmon.merged.gene_counts_length_scaled.tsv", - "salmon.merged.gene_counts_scaled.SummarizedExperiment.rds", - "salmon.merged.gene_counts_scaled.tsv", - "salmon.merged.gene_lengths.tsv", - "salmon.merged.gene_tpm.tsv", - "salmon.merged.transcript_counts.SummarizedExperiment.rds", - "salmon.merged.transcript_counts.tsv", - "salmon.merged.transcript_lengths.tsv", - "salmon.merged.transcript_tpm.tsv", - "tx2gene.tsv", + "salmon/RAP1_IAA_30M_REP1", + "salmon/RAP1_IAA_30M_REP1/aux_info", + "salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv", + "salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz", + "salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz", + "salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json", + "salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz", + "salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz", + "salmon/RAP1_IAA_30M_REP1/cmd_info.json", + "salmon/RAP1_IAA_30M_REP1/libParams", + "salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt", + "salmon/RAP1_IAA_30M_REP1/lib_format_counts.json", + "salmon/RAP1_IAA_30M_REP1/logs", + "salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log", + "salmon/RAP1_IAA_30M_REP1/quant.genes.sf", + "salmon/RAP1_IAA_30M_REP1/quant.sf", + "salmon/RAP1_UNINDUCED_REP1", + "salmon/RAP1_UNINDUCED_REP1/aux_info", + "salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv", + "salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz", + "salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz", + "salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json", + "salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz", + "salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz", + "salmon/RAP1_UNINDUCED_REP1/cmd_info.json", + "salmon/RAP1_UNINDUCED_REP1/libParams", + "salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt", + "salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json", + "salmon/RAP1_UNINDUCED_REP1/logs", + "salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log", + "salmon/RAP1_UNINDUCED_REP1/quant.genes.sf", + "salmon/RAP1_UNINDUCED_REP1/quant.sf", + "salmon/RAP1_UNINDUCED_REP2", + "salmon/RAP1_UNINDUCED_REP2/aux_info", + "salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv", + "salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz", + "salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz", + "salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json", + "salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz", + "salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz", + "salmon/RAP1_UNINDUCED_REP2/cmd_info.json", + "salmon/RAP1_UNINDUCED_REP2/libParams", + "salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt", + "salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json", + "salmon/RAP1_UNINDUCED_REP2/logs", + "salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log", + "salmon/RAP1_UNINDUCED_REP2/quant.genes.sf", + "salmon/RAP1_UNINDUCED_REP2/quant.sf", + "salmon/WT_REP1", + "salmon/WT_REP1/aux_info", + "salmon/WT_REP1/aux_info/ambig_info.tsv", + "salmon/WT_REP1/aux_info/expected_bias.gz", + "salmon/WT_REP1/aux_info/fld.gz", + "salmon/WT_REP1/aux_info/meta_info.json", + "salmon/WT_REP1/aux_info/observed_bias.gz", + "salmon/WT_REP1/aux_info/observed_bias_3p.gz", + "salmon/WT_REP1/cmd_info.json", + "salmon/WT_REP1/libParams", + "salmon/WT_REP1/libParams/flenDist.txt", + "salmon/WT_REP1/lib_format_counts.json", + "salmon/WT_REP1/logs", + "salmon/WT_REP1/logs/salmon_quant.log", + "salmon/WT_REP1/quant.genes.sf", + "salmon/WT_REP1/quant.sf", + "salmon/WT_REP2", + "salmon/WT_REP2/aux_info", + "salmon/WT_REP2/aux_info/ambig_info.tsv", + "salmon/WT_REP2/aux_info/expected_bias.gz", + "salmon/WT_REP2/aux_info/fld.gz", + "salmon/WT_REP2/aux_info/meta_info.json", + "salmon/WT_REP2/aux_info/observed_bias.gz", + "salmon/WT_REP2/aux_info/observed_bias_3p.gz", + "salmon/WT_REP2/cmd_info.json", + "salmon/WT_REP2/libParams", + "salmon/WT_REP2/libParams/flenDist.txt", + "salmon/WT_REP2/lib_format_counts.json", + "salmon/WT_REP2/logs", + "salmon/WT_REP2/logs/salmon_quant.log", + "salmon/WT_REP2/quant.genes.sf", + "salmon/WT_REP2/quant.sf", + "salmon/salmon.merged.gene_counts.SummarizedExperiment.rds", + "salmon/salmon.merged.gene_counts.tsv", + "salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds", + "salmon/salmon.merged.gene_counts_length_scaled.tsv", + "salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds", + "salmon/salmon.merged.gene_counts_scaled.tsv", + "salmon/salmon.merged.gene_lengths.tsv", + "salmon/salmon.merged.gene_tpm.tsv", + "salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds", + "salmon/salmon.merged.transcript_counts.tsv", + "salmon/salmon.merged.transcript_lengths.tsv", + "salmon/salmon.merged.transcript_tpm.tsv", + "salmon/tx2gene.tsv", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -340,7 +340,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:40:28.607731" + "timestamp": "2024-10-02T08:10:56.056197" }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ @@ -383,26 +383,26 @@ }, [ "custom", - "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", "fastqc", - "trim", + "fastqc/trim", "multiqc", - "multiqc_data", - "multiqc_plots", - "multiqc_report.html", + "multiqc/multiqc_data", + "multiqc/multiqc_plots", + "multiqc/multiqc_report.html", "pipeline_info", - "nf_core_rnaseq_software_mqc_versions.yml", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -413,6 +413,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:41:05.28637" + "timestamp": "2024-10-02T08:11:32.236118" } } \ No newline at end of file diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index 74e09f92d..3c03631cc 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 316818792..ff25d5c62 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -45,27 +45,27 @@ }, [ "custom", - "out", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", "fastqc", - "trim", + "fastqc/trim", "multiqc", - "star_salmon", - "multiqc_data", - "multiqc_plots", - "multiqc_report.html", + "multiqc/star_salmon", + "multiqc/star_salmon/multiqc_data", + "multiqc/star_salmon/multiqc_plots", + "multiqc/star_salmon/multiqc_report.html", "pipeline_info", - "nf_core_rnaseq_software_mqc_versions.yml", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -76,7 +76,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:47:43.501368" + "timestamp": "2024-10-02T08:17:45.954114" }, "Params: --skip_qc": { "content": [ @@ -174,503 +174,503 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt", + "bbsplit/RAP1_IAA_30M_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP2.stats.txt", + "bbsplit/WT_REP1.stats.txt", + "bbsplit/WT_REP2.stats.txt", "custom", - "out", - "genome_gfp.fasta", - "genome_gfp.gtf", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", "fastqc", - "trim", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", - "WT_REP1_trimmed_1_val_1_fastqc.html", - "WT_REP1_trimmed_1_val_1_fastqc.zip", - "WT_REP1_trimmed_2_val_2_fastqc.html", - "WT_REP1_trimmed_2_val_2_fastqc.zip", - "WT_REP2_trimmed_1_val_1_fastqc.html", - "WT_REP2_trimmed_1_val_1_fastqc.zip", - "WT_REP2_trimmed_2_val_2_fastqc.html", - "WT_REP2_trimmed_2_val_2_fastqc.zip", + "fastqc/trim", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip", "multiqc", - "star_salmon", - "multiqc_report.html", - "multiqc_report_data", - "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "fastqc-status-check-heatmap.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", - "fastqc_top_overrepresented_sequences_table.txt", - "multiqc_citations.txt", - "multiqc_cutadapt.txt", - "multiqc_data.json", - "multiqc_fastqc_fastqc_trimmed.txt", - "multiqc_general_stats.txt", - "multiqc_picard_dups.txt", - "multiqc_salmon.txt", - "multiqc_samtools_flagstat.txt", - "multiqc_samtools_idxstats.txt", - "multiqc_samtools_stats.txt", - "multiqc_software_versions.txt", - "multiqc_sources.txt", - "multiqc_star.txt", - "picard_deduplication.txt", - "picard_histogram.txt", - "picard_histogram_1.txt", - "picard_histogram_2.txt", - "salmon_plot.txt", - "samtools-flagstat-dp_Percentage_of_total.txt", - "samtools-flagstat-dp_Read_counts.txt", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", - "samtools-stats-dp.txt", - "samtools_alignment_plot.txt", - "star_alignment_plot.txt", - "star_summary_table.txt", - "multiqc_report_plots", - "pdf", - "cutadapt_filtered_reads_plot-cnt.pdf", - "cutadapt_filtered_reads_plot-pct.pdf", - "cutadapt_trimmed_sequences_plot_3_Counts.pdf", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "fastqc-status-check-heatmap.pdf", - "fastqc_overrepresented_sequences_plot.pdf", - "fastqc_per_base_n_content_plot.pdf", - "fastqc_per_base_sequence_quality_plot.pdf", - "fastqc_per_sequence_gc_content_plot_Counts.pdf", - "fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "fastqc_per_sequence_quality_scores_plot.pdf", - "fastqc_sequence_counts_plot-cnt.pdf", - "fastqc_sequence_counts_plot-pct.pdf", - "fastqc_sequence_duplication_levels_plot.pdf", - "fastqc_sequence_length_distribution_plot.pdf", - "fastqc_top_overrepresented_sequences_table.pdf", - "general_stats_table.pdf", - "picard_deduplication-cnt.pdf", - "picard_deduplication-pct.pdf", - "salmon_plot.pdf", - "samtools-flagstat-dp_Percentage_of_total.pdf", - "samtools-flagstat-dp_Read_counts.pdf", - "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", - 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+ "star_salmon/WT_REP1/aux_info", + "star_salmon/WT_REP1/aux_info/ambig_info.tsv", + "star_salmon/WT_REP1/aux_info/expected_bias.gz", + "star_salmon/WT_REP1/aux_info/fld.gz", + "star_salmon/WT_REP1/aux_info/meta_info.json", + "star_salmon/WT_REP1/aux_info/observed_bias.gz", + "star_salmon/WT_REP1/aux_info/observed_bias_3p.gz", + "star_salmon/WT_REP1/cmd_info.json", + "star_salmon/WT_REP1/libParams", + "star_salmon/WT_REP1/libParams/flenDist.txt", + "star_salmon/WT_REP1/logs", + "star_salmon/WT_REP1/logs/salmon_quant.log", + "star_salmon/WT_REP1/quant.genes.sf", + "star_salmon/WT_REP1/quant.sf", + "star_salmon/WT_REP2", + "star_salmon/WT_REP2.markdup.sorted.bam", + "star_salmon/WT_REP2.markdup.sorted.bam.bai", + "star_salmon/WT_REP2/aux_info", + "star_salmon/WT_REP2/aux_info/ambig_info.tsv", + "star_salmon/WT_REP2/aux_info/expected_bias.gz", + "star_salmon/WT_REP2/aux_info/fld.gz", + "star_salmon/WT_REP2/aux_info/meta_info.json", + "star_salmon/WT_REP2/aux_info/observed_bias.gz", + "star_salmon/WT_REP2/aux_info/observed_bias_3p.gz", + "star_salmon/WT_REP2/cmd_info.json", + "star_salmon/WT_REP2/libParams", + "star_salmon/WT_REP2/libParams/flenDist.txt", + "star_salmon/WT_REP2/logs", + "star_salmon/WT_REP2/logs/salmon_quant.log", + "star_salmon/WT_REP2/quant.genes.sf", + "star_salmon/WT_REP2/quant.sf", + "star_salmon/bigwig", + "star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig", + "star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig", + "star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig", + "star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig", + "star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig", + "star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig", + "star_salmon/bigwig/WT_REP1.forward.bigWig", + "star_salmon/bigwig/WT_REP1.reverse.bigWig", + "star_salmon/bigwig/WT_REP2.forward.bigWig", + "star_salmon/bigwig/WT_REP2.reverse.bigWig", + "star_salmon/log", + "star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out", + "star_salmon/log/RAP1_IAA_30M_REP1.Log.out", + "star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out", + "star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab", + "star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out", + "star_salmon/log/RAP1_UNINDUCED_REP1.Log.out", + "star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out", + "star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab", + "star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out", + "star_salmon/log/RAP1_UNINDUCED_REP2.Log.out", + "star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out", + "star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab", + "star_salmon/log/WT_REP1.Log.final.out", + "star_salmon/log/WT_REP1.Log.out", + "star_salmon/log/WT_REP1.Log.progress.out", + "star_salmon/log/WT_REP1.SJ.out.tab", + "star_salmon/log/WT_REP2.Log.final.out", + "star_salmon/log/WT_REP2.Log.out", + "star_salmon/log/WT_REP2.Log.progress.out", + "star_salmon/log/WT_REP2.SJ.out.tab", + "star_salmon/picard_metrics", + "star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", + "star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt", + "star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt", + "star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt", + "star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt", + "star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts.tsv", + "star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts_length_scaled.tsv", + "star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts_scaled.tsv", + "star_salmon/salmon.merged.gene_lengths.tsv", + "star_salmon/salmon.merged.gene_tpm.tsv", + "star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds", + "star_salmon/salmon.merged.transcript_counts.tsv", + "star_salmon/salmon.merged.transcript_lengths.tsv", + "star_salmon/salmon.merged.transcript_tpm.tsv", + "star_salmon/samtools_stats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.stats", + "star_salmon/stringtie", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf", + "star_salmon/stringtie/WT_REP1.ballgown", + "star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/WT_REP1.coverage.gtf", + "star_salmon/stringtie/WT_REP1.gene.abundance.txt", + "star_salmon/stringtie/WT_REP1.transcripts.gtf", + "star_salmon/stringtie/WT_REP2.ballgown", + "star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/WT_REP2.coverage.gtf", + "star_salmon/stringtie/WT_REP2.gene.abundance.txt", + "star_salmon/stringtie/WT_REP2.transcripts.gtf", + "star_salmon/tx2gene.tsv", "trimgalore", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -804,6 +804,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:46:49.794228" + "timestamp": "2024-10-02T08:17:03.577873" } } \ No newline at end of file diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index b7600628f..5053e103f 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 8591548f9..bbdcc5a51 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -135,981 +135,981 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt", + "bbsplit/RAP1_IAA_30M_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP2.stats.txt", + "bbsplit/WT_REP1.stats.txt", + "bbsplit/WT_REP2.stats.txt", "custom", - "out", - "genome_gfp.fasta", - "genome_gfp.gtf", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", "fastqc", - "raw", - "RAP1_IAA_30M_REP1_raw_1_fastqc.html", - "RAP1_IAA_30M_REP1_raw_1_fastqc.zip", - "RAP1_IAA_30M_REP1_raw_2_fastqc.html", - "RAP1_IAA_30M_REP1_raw_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_raw_fastqc.html", - "RAP1_UNINDUCED_REP1_raw_fastqc.zip", - "RAP1_UNINDUCED_REP2_raw_fastqc.html", - "RAP1_UNINDUCED_REP2_raw_fastqc.zip", - "WT_REP1_raw_1_fastqc.html", - "WT_REP1_raw_1_fastqc.zip", - "WT_REP1_raw_2_fastqc.html", - "WT_REP1_raw_2_fastqc.zip", - "WT_REP2_raw_1_fastqc.html", - "WT_REP2_raw_1_fastqc.zip", - "WT_REP2_raw_2_fastqc.html", - "WT_REP2_raw_2_fastqc.zip", + "fastqc/raw", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip", + "fastqc/raw/WT_REP1_raw_1_fastqc.html", + "fastqc/raw/WT_REP1_raw_1_fastqc.zip", + "fastqc/raw/WT_REP1_raw_2_fastqc.html", + "fastqc/raw/WT_REP1_raw_2_fastqc.zip", + "fastqc/raw/WT_REP2_raw_1_fastqc.html", + "fastqc/raw/WT_REP2_raw_1_fastqc.zip", + "fastqc/raw/WT_REP2_raw_2_fastqc.html", + "fastqc/raw/WT_REP2_raw_2_fastqc.zip", "multiqc", - "star_salmon", - "multiqc_report.html", - "multiqc_report_data", - "fastqc-status-check-heatmap.txt", - "fastqc_adapter_content_plot.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_top_overrepresented_sequences_table.txt", - "junction_saturation_known.txt", - "junction_saturation_novel.txt", - "multiqc_citations.txt", - "multiqc_data.json", - "multiqc_dupradar-section-plot.txt", - "multiqc_fail_strand_check_table.txt", - "multiqc_fastqc_fastqc_raw.txt", - "multiqc_featurecounts_biotype_plot.txt", - "multiqc_general_stats.txt", - "multiqc_picard_dups.txt", - "multiqc_rseqc_bam_stat.txt", - "multiqc_rseqc_infer_experiment.txt", - "multiqc_rseqc_junction_annotation.txt", - "multiqc_rseqc_read_distribution.txt", - "multiqc_salmon.txt", - "multiqc_salmon_deseq2_clustering-plot.txt", - "multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc_salmon_deseq2_clustering-plot_4.txt", - "multiqc_salmon_deseq2_pca-plot.txt", - "multiqc_samtools_flagstat.txt", - "multiqc_samtools_idxstats.txt", - "multiqc_samtools_stats.txt", - "multiqc_software_versions.txt", - "multiqc_sources.txt", - "multiqc_star.txt", - "multiqc_star_salmon_deseq2_clustering-plot.txt", - "multiqc_star_salmon_deseq2_clustering-plot_1.txt", - "multiqc_star_salmon_deseq2_clustering-plot_2.txt", - "multiqc_star_salmon_deseq2_clustering-plot_3.txt", - "multiqc_star_salmon_deseq2_clustering-plot_4.txt", - "multiqc_star_salmon_deseq2_pca-plot.txt", - "picard_deduplication.txt", - "picard_histogram.txt", - "picard_histogram_1.txt", - "picard_histogram_2.txt", - "qualimap_gene_coverage_profile_Counts.txt", - "qualimap_gene_coverage_profile_Normalised.txt", - "qualimap_genomic_origin.txt", - "qualimap_rnaseq_cov_hist.txt", - "qualimap_rnaseq_genome_results.txt", - "rseqc_bam_stat.txt", - "rseqc_infer_experiment_plot.txt", - "rseqc_inner_distance.txt", - "rseqc_inner_distance_plot_Counts.txt", - "rseqc_inner_distance_plot_Percentages.txt", - "rseqc_junction_annotation_junctions_plot_Events.txt", - "rseqc_junction_annotation_junctions_plot_Junctions.txt", - "rseqc_junction_saturation_all.txt", - "rseqc_junction_saturation_plot_All_Junctions.txt", - "rseqc_junction_saturation_plot_Known_Junctions.txt", - "rseqc_junction_saturation_plot_Novel_Junctions.txt", - 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"star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt", + "star_salmon/rseqc/read_duplication", + "star_salmon/rseqc/read_duplication/pdf", + "star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf", + "star_salmon/rseqc/read_duplication/rscript", + "star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r", + "star_salmon/rseqc/read_duplication/xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls", + "star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls", + "star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts.tsv", + "star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts_length_scaled.tsv", + "star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds", + "star_salmon/salmon.merged.gene_counts_scaled.tsv", + "star_salmon/salmon.merged.gene_lengths.tsv", + "star_salmon/salmon.merged.gene_tpm.tsv", + "star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds", + "star_salmon/salmon.merged.transcript_counts.tsv", + "star_salmon/salmon.merged.transcript_lengths.tsv", + "star_salmon/salmon.merged.transcript_tpm.tsv", + "star_salmon/samtools_stats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats", + "star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP1.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats", + "star_salmon/samtools_stats/WT_REP2.sorted.bam.stats", + "star_salmon/stringtie", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt", + "star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt", + "star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf", + "star_salmon/stringtie/WT_REP1.ballgown", + "star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab", + "star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab", + "star_salmon/stringtie/WT_REP1.coverage.gtf", + "star_salmon/stringtie/WT_REP1.gene.abundance.txt", + "star_salmon/stringtie/WT_REP1.transcripts.gtf", + "star_salmon/stringtie/WT_REP2.ballgown", + "star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab", + "star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab", + "star_salmon/stringtie/WT_REP2.coverage.gtf", + "star_salmon/stringtie/WT_REP2.gene.abundance.txt", + "star_salmon/stringtie/WT_REP2.transcripts.gtf", + "star_salmon/tx2gene.tsv" ], [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", @@ -1379,6 +1379,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T19:54:39.111945" + "timestamp": "2024-10-02T08:24:30.328195" } } \ No newline at end of file diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 6e5e60425..268a1fabb 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -24,8 +24,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } @@ -56,8 +56,8 @@ nextflow_pipeline { workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - // All stable path name - stable_name*.name, + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), // All files with stable contents stable_path ).match() } diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index c9881f337..b4e4f981b 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -139,1002 +139,1002 @@ }, [ "bbsplit", - "RAP1_IAA_30M_REP1.stats.txt", - "RAP1_UNINDUCED_REP1.stats.txt", - "RAP1_UNINDUCED_REP2.stats.txt", - "WT_REP1.stats.txt", - "WT_REP2.stats.txt", + "bbsplit/RAP1_IAA_30M_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP1.stats.txt", + "bbsplit/RAP1_UNINDUCED_REP2.stats.txt", + "bbsplit/WT_REP1.stats.txt", + "bbsplit/WT_REP2.stats.txt", "custom", - "out", - "genome_gfp.fasta", - "genome_gfp.gtf", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", "fastqc", - "raw", - "RAP1_IAA_30M_REP1_raw_1_fastqc.html", - "RAP1_IAA_30M_REP1_raw_1_fastqc.zip", - "RAP1_IAA_30M_REP1_raw_2_fastqc.html", - "RAP1_IAA_30M_REP1_raw_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_raw_fastqc.html", - "RAP1_UNINDUCED_REP1_raw_fastqc.zip", - "RAP1_UNINDUCED_REP2_raw_fastqc.html", - "RAP1_UNINDUCED_REP2_raw_fastqc.zip", - "WT_REP1_raw_1_fastqc.html", - "WT_REP1_raw_1_fastqc.zip", - "WT_REP1_raw_2_fastqc.html", - "WT_REP1_raw_2_fastqc.zip", - "WT_REP2_raw_1_fastqc.html", - "WT_REP2_raw_1_fastqc.zip", - "WT_REP2_raw_2_fastqc.html", - "WT_REP2_raw_2_fastqc.zip", - "trim", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", - "WT_REP1_trimmed_1_val_1_fastqc.html", - "WT_REP1_trimmed_1_val_1_fastqc.zip", - "WT_REP1_trimmed_2_val_2_fastqc.html", - "WT_REP1_trimmed_2_val_2_fastqc.zip", - "WT_REP2_trimmed_1_val_1_fastqc.html", - "WT_REP2_trimmed_1_val_1_fastqc.zip", - "WT_REP2_trimmed_2_val_2_fastqc.html", - "WT_REP2_trimmed_2_val_2_fastqc.zip", + "fastqc/raw", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html", + "fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html", + "fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html", + "fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip", + "fastqc/raw/WT_REP1_raw_1_fastqc.html", + "fastqc/raw/WT_REP1_raw_1_fastqc.zip", + "fastqc/raw/WT_REP1_raw_2_fastqc.html", + "fastqc/raw/WT_REP1_raw_2_fastqc.zip", + "fastqc/raw/WT_REP2_raw_1_fastqc.html", + "fastqc/raw/WT_REP2_raw_1_fastqc.zip", + "fastqc/raw/WT_REP2_raw_2_fastqc.html", + "fastqc/raw/WT_REP2_raw_2_fastqc.zip", + "fastqc/trim", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html", + "fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip", "multiqc", - "star_rsem", - "multiqc_report.html", - "multiqc_report_data", - "cutadapt_filtered_reads_plot.txt", - "cutadapt_trimmed_sequences_plot_3_Counts.txt", - "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "fastqc-status-check-heatmap-1.txt", - "fastqc-status-check-heatmap.txt", - "fastqc_adapter_content_plot.txt", - "fastqc_overrepresented_sequences_plot-1.txt", - "fastqc_overrepresented_sequences_plot.txt", - "fastqc_per_base_n_content_plot-1.txt", - "fastqc_per_base_n_content_plot.txt", - "fastqc_per_base_sequence_quality_plot-1.txt", - "fastqc_per_base_sequence_quality_plot.txt", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "fastqc_per_sequence_gc_content_plot_Counts.txt", - "fastqc_per_sequence_gc_content_plot_Percentages.txt", - "fastqc_per_sequence_quality_scores_plot-1.txt", - "fastqc_per_sequence_quality_scores_plot.txt", - "fastqc_sequence_counts_plot-1.txt", - "fastqc_sequence_counts_plot.txt", - "fastqc_sequence_duplication_levels_plot-1.txt", - "fastqc_sequence_duplication_levels_plot.txt", - "fastqc_sequence_length_distribution_plot.txt", - "fastqc_top_overrepresented_sequences_table-1.txt", - "fastqc_top_overrepresented_sequences_table.txt", 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}, - "hisat2/markdup": { - "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", - "WT_REP1.markdup.sorted.bam", - "WT_REP1.markdup.sorted.bam.bai", - "WT_REP2.markdup.sorted.bam", - "WT_REP2.markdup.sorted.bam.bai" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T13:40:29.820359" -======= "timestamp": "2024-10-02T07:43:07.13584" ->>>>>>> dev } } From 00a0857b9292d15f65fa99fb853282367e0bfb19 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Wed, 2 Oct 2024 14:21:02 +0200 Subject: [PATCH 100/100] Apply suggestions from code review Co-authored-by: James A. Fellows Yates --- subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf index 5d55ce0a8..cb051a38c 100644 --- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf @@ -259,7 +259,7 @@ def validateInputParameters() { //General checks for if contaminant screening is used if (params.contaminant_screening) { if (params.aligner == 'star_rsem') { - error("Contaminant screeneing cannot be done with --aligner star_rsem since unaligned reads are not saved. Please use --aligner star_salmon or --aligner hisat2.") + error("Contaminant screening cannot be done with --aligner star_rsem since unaligned reads are not saved. Please use --aligner star_salmon or --aligner hisat2.") } } @@ -268,7 +268,7 @@ def validateInputParameters() { if (!params.kraken_db) { error("Contaminant screening set to kraken2 but not database is provided. Please provide a database with the --kraken_db option.") } - //Check that Kraken/Bracken parameters are not provided when Kraken2 is not being used + // Check that Kraken/Bracken parameters are not provided when Kraken2 is not being used } else { if (!params.bracken_precision.equals('S')) { brackenPrecisionWithoutKrakenDBWarn()

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zR}&jm{kHrg-P@Ua{y*RHwe`*a<1P5}EyLUV_xb<#r)=2J@8AEwkNHQ7|3AO2X}$mV iA^&?e|M%U=@^uYkzvlR?pMOZ<%h+hb$P**1H~cTIV!x&U diff --git a/docs/images/nf-core-rnaseq_metro_map_grey.svg b/docs/images/nf-core-rnaseq_metro_map_grey.svg index 46be07297..2eb57fe62 100644 --- a/docs/images/nf-core-rnaseq_metro_map_grey.svg +++ b/docs/images/nf-core-rnaseq_metro_map_grey.svg @@ -7,7 +7,7 @@ viewBox="0 0 646.4851 269.92565" version="1.1" id="svg8" - inkscape:version="1.3.2 (1:1.3.2+202311252150+091e20ef0f)" + inkscape:version="1.3.2 (091e20e, 2023-11-25)" sodipodi:docname="nf-core-rnaseq_metro_map_grey.svg" inkscape:export-filename="nf-core-rnaseq_metro_map_grey.png" inkscape:export-xdpi="89" @@ -21,7 +21,22 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:cc="http://creativecommons.org/ns#" xmlns:dc="http://purl.org/dc/elements/1.1/">catcatfastqfastqsubsamplefastq(fq)5RSeQC(multiple modules)PreseqdupRadarKraken2/BrackenDESeq2(PCA only)MultiQCQualimaprnaseqrnaseqSortMeRNAFastQCinferstrandedness(fq, Salmon)(Salmon)BBSplit Date: Mon, 19 Aug 2024 11:59:33 -0400 Subject: [PATCH 027/100] Update schema --- nextflow_schema.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index b524e762f..a8c29c97f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -561,7 +561,7 @@ "kraken_db": { "type": "string", "description": "Database when using Kraken2/Bracken for contaminant screening.", - "help_text": "See [pre-built Kraken2/Bracken databases](https://benlangmead.github.io/aws-indexes/k2).", + "help_text": "See the usage tab for more information", "fa_icon": "fas fa-fish" }, "bracken_precision": { @@ -569,6 +569,7 @@ "default": "S", "fa_icon": "fas fa-tree", "description": "Taxonomic level for Bracken abundance estimations.", + "help_text": "First letter of Domain / Phylum / Class / Order / Family / Genus / Species", "enum": ["D", "P", "C", "O", "F", "G", "S"] } } From 75a10f7f119da07108563a79c15efcc9596d9ae9 Mon Sep 17 00:00:00 2001 From: Ezra Greenberg <120955867+egreenberg7@users.noreply.github.com> Date: Mon, 19 Aug 2024 12:01:54 -0400 Subject: [PATCH 028/100] Update docs/usage.md Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com> --- docs/usage.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index a86387066..cd42a399b 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -298,7 +298,11 @@ By default, the input GTF file will be filtered to ensure that sequence names co ## Contamination screening options -The pipeline provides the option to scan unaligned reads for contamination from other species by using [Kraken2](https://ccb.jhu.edu/software/kraken2/) with or without corrections from [Bracken](https://ccb.jhu.edu/software/bracken/). As Bracken is not a particularly expensive algorithm, we recommend using it to correct the abundance estimations from Kraken. An important note is that Kraken2 is [sensitive to the database](https://doi.org/10.1099/mgen.0.000949) that it is used with. It is [particularly important](https://doi.org/10.1128/mbio.01607-23) to ensure that the host genome is part of the database, and if you are particularly concerned about specific contaminants, it may be worthwhile to use a smaller database that contains primarily those contaminants rather than the full standard database. Various pre-built databases can be found [here](https://benlangmead.github.io/aws-indexes/k2) and instructions for building a custom database can be found at the [Kraken2 documentation](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown). Genomes of contaminants detected in previous sequencing experiments can be found on the [OpenContami website](https://openlooper.hgc.jp/opencontami/help/help_oct.php). Additionally, note that while one of the primary strengths of Kraken2 is that it can detect low abundance contaminants in a sample, false positives can also occur. If a very low number of reads of some contaminating species is detected, these results should be treated with caution. +The pipeline provides the option to scan unaligned reads for contamination from other species using [Kraken2](https://ccb.jhu.edu/software/kraken2/), with the possibility of applying corrections from [Bracken](https://ccb.jhu.edu/software/bracken/). Since running Bracken is not computationally expensive, we recommend always using it to refine the abundance estimates generated by Kraken2. + +It is important to note that the accuracy of Kraken2 is [highly dependent on the database](https://doi.org/10.1099/mgen.0.000949) used. Specifically, it is [crucial](https://doi.org/10.1128/mbio.01607-23) to ensure that the host genome is included in the database. If you are particularly concerned about certain contaminants, it may be beneficial to use a smaller, more focused database containing primarily those contaminants instead of the full standard database. Various pre-built databases [are available for download](https://benlangmead.github.io/aws-indexes/k2), and instructions for building a custom database can be found in the [Kraken2 documentation](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown). Additionally, genomes of contaminants detected in previous sequencing experiments are available on the [OpenContami website](https://openlooper.hgc.jp/opencontami/help/help_oct.php). + +While Kraken2 is capable of detecting low-abundance contaminants in a sample, false positives can occur. Therefore, if only a very small number of reads from a contaminating species are detected, these results should be interpreted with caution. ## Running the pipeline From cfc89458ad3ab931eb0dfd313a2d19dcf61308bb Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Mon, 19 Aug 2024 12:42:26 -0400 Subject: [PATCH 029/100] Change output directory for kraken2/bracken --- docs/output.md | 4 ++-- modules/nf-core/bracken/bracken/nextflow.config | 2 +- modules/nf-core/kraken2/kraken2/nextflow.config | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/output.md b/docs/output.md index 144caabd5..068a5db17 100644 --- a/docs/output.md +++ b/docs/output.md @@ -660,11 +660,11 @@ The plot on the left hand side shows the standard PC plot - notice the variable