diff --git a/CHANGELOG.md b/CHANGELOG.md index cd24663bd..8de447e70 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,11 +3,62 @@ 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). +## [[3.16.0](https://github.com/nf-core/rnaseq/releases/tag/3.16.0)] - 2024-10-02 + +### 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 +- [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 + +| 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 - [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 - [PR #1382](https://github.com/nf-core/rnaseq/pull/1381) - Slight fixes for rnaseq preprocessing 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. 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 000000000..ac2d485f6 Binary files /dev/null and b/docs/images/bracken-top-n-plot.png differ diff --git a/docs/images/nf-core-rnaseq_metro_map_grey.png b/docs/images/nf-core-rnaseq_metro_map_grey.png index d2c040315..79b4e2afc 100644 Binary files a/docs/images/nf-core-rnaseq_metro_map_grey.png and b/docs/images/nf-core-rnaseq_metro_map_grey.png differ diff --git a/docs/images/nf-core-rnaseq_metro_map_grey.svg b/docs/images/nf-core-rnaseq_metro_map_grey.svg index 7b55ae7e5..2de5cd2e3 100644 --- a/docs/images/nf-core-rnaseq_metro_map_grey.svg +++ b/docs/images/nf-core-rnaseq_metro_map_grey.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/">1catfastqSTAGE2. Genome alignment & quantification3. Pseudo-alignment & quantification1. Pre-processing4. Post-processing3SalmonKallistoMultiQCTSV5RSeQC(multiple modules)Preseq GermlineSarek  Exome GermlineSarek  Exome GermlineSarek BIGWIGHTMLHTML ExomedupRadar GermlineSarek BAMBAIPseudo-aligner: Salmon, Quantification: SalmonAligner: HISAT2, Quantification: NoneAligner: STAR, Quantification: Salmon (default)Pseudo-aligner: Kallisto, Quantification: KallistoAligner: STAR, Quantification: RSEMMETHODLicense:STAGE2. Genome alignment & quantification3. Pseudo-alignment & quantification5. Final QC1. Pre-processing4. Post-processingGTFFASTAFASTQcatfastqTrimGalore!SortMeRNAFastQCinferstrandedness(fq, Salmon)BBSplitUMI-toolsextractFastQC1catfastqSTAGE2. Genome alignment & quantification3. Pseudo-alignment & quantification1. Pre-processing4. Post-processing35412 +  GermlineSarek  Exome GermlineSarek TSV Exome GermlineSarek  + id="flowRoot4845-2-2-4-4-4" + style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;line-height:0.01%;font-family:Chandas;-inkscape-font-specification:Chandas;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"> 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"> diff --git a/docs/output.md b/docs/output.md index bb2f03f6b..fe3757ad7 100644 --- a/docs/output.md +++ b/docs/output.md @@ -40,6 +40,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [Preseq](#preseq) - Estimation of library complexity - [featureCounts](#featurecounts) - Read counting relative to gene biotype - [DESeq2](#deseq2) - PCA plot and sample pairwise distance heatmap and dendrogram + - [Kraken2/Bracken](#kraken2bracken) - Taxonomic classification of unaligned reads - [MultiQC](#multiqc) - Present QC for raw reads, alignment, read counting and sample similiarity - [Pseudoalignment and quantification](#pseudoalignment-and-quantification) - [Salmon](#pseudoalignment) - Wicked fast gene and isoform quantification relative to the transcriptome @@ -656,6 +657,25 @@ The plot on the left hand side shows the standard PC plot - notice the variable

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..c351786e2 100644 --- a/modules.json +++ b/modules.json @@ -13,6 +13,12 @@ "bedtools/genomecov": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "installed_by": ["modules"], + "patch": "modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff" + }, + "bracken/bracken": { + "branch": "master", + "git_sha": "c214fad97b328eb6d6233f779be9ba44814a9136", "installed_by": ["modules"] }, "cat/fastq": { @@ -68,7 +74,8 @@ "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 +97,11 @@ "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/bedtools/genomecov/bedtools-genomecov.diff b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff new file mode 100644 index 000000000..53d7e34df --- /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 +@@ -4,8 +4,8 @@ + + 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' }" ++ 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': ++ '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..91869ec23 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -4,8 +4,8 @@ process BEDTOOLS_GENOMECOV { 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' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': + 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" input: tuple val(meta), path(intervals), val(scale) 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..2a64e4f4f --- /dev/null +++ b/modules/nf-core/hisat2/align/hisat2-align.diff @@ -0,0 +1,57 @@ +Changes in module 'nf-core/hisat2/align' +--- modules/nf-core/hisat2/align/main.nf ++++ modules/nf-core/hisat2/align/main.nf +@@ -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) { +- 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 @@ + 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 ${prefix}.unmapped.fastq.gz" : '' + """ + INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\\.1.ht2\$//'` + hisat2 \\ +@@ -91,7 +91,8 @@ + + stub: + def prefix = task.ext.prefix ?: "${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 d4bd05ca3..d2b1f40a9 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 @@ -340,7 +345,7 @@ manifest { description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '3.15.1' + version = '3.16.0' doi = 'https://doi.org/10.5281/zenodo.1400710' } 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/nf-test.config b/nf-test.config index 0f4cac519..c843dabec 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@0.0.2" } } 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..cb051a38c 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 screening 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/tests/.nftignore b/tests/.nftignore new file mode 100644 index 000000000..dcbd8d8a8 --- /dev/null +++ b/tests/.nftignore @@ -0,0 +1,125 @@ +**/*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 +**/*markdup.sorted.{bam,bam.bai} +**/*read_distribution.txt +**/*sorted.bam.{flagstat,idxstats,stats} +**/*sortmerna.log +**/*splice_{events,junction}.{pdf,png,svg} +**/*transcripts.gtf +**/*{cnt,model,theta} +**/*{css,gif,js} +**/*{forward,reverse}.bigWig +**/*{genes,isoforms}.results +**/*{pos,seq}.DupRate.xls +**/*{salmon,star_salmon,star_rsem}_deseq2_clustering-plot*{pdf,png,txt} +**/Junction*.png +**/Reads*.png +**/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_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} +bbsplit/*.stats.txt +pipeline_info/*.{html,json,txt,yml} +**/deseq2_qc/size_factors/*.txt +star_rsem/log/*.log diff --git a/tests/default.nf.test b/tests/default.nf.test index 069bb846f..80b19646a 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -12,908 +12,22 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${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 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") } + { 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 + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), + // All files with stable contents + stable_path + ).match() } ) } } @@ -929,31 +43,21 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.removeNextflowVersion("$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("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // 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 eb727b082..296b93241 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,1080 +1,1598 @@ { - "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": "2024-08-22T14:57:58.85709" - }, - "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", - 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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" + "nextflow": "24.08.0" }, - "timestamp": "2024-08-26T12:44:57.740534" + "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 16794293b..fcd11c1da 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -13,878 +13,22 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${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, - 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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/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("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") - ).match("versions") } + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), + // All files with stable contents + stable_path + ).match() } ) } } @@ -901,31 +45,21 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.removeNextflowVersion("$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("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // 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 4bb12f76b..ee17ab23d 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -1,1044 +1,1546 @@ { - "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", - 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"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", + "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.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", + "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", + "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" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T14:18:38.410297" + "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 9577086ea..e743a37d4 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -13,806 +13,22 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${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 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") } + { 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 + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), + // All files with stable contents + stable_path + ).match() } ) } } @@ -829,31 +45,21 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.removeNextflowVersion("$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("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // 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 734ca3040..4de59e1ae 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -1,961 +1,1444 @@ { - "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" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T12:35:11.735947" - }, - "references": { - "content": [ - "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", - "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T10:32:15.597034" - }, - "hisat2/featurecounts": { - "content": [ - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,079b099e5c5e9fe5e2559dfc938aa48b", - "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", - "RAP1_IAA_30M_REP1.featureCounts.txt:md5,eedff929765dbc950528ee499e6d63ba", - "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,4d1820a35481f454f17a14326356253d", - "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", - "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,b007abbc78b08d8d2bb37a267665947d", - "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,3632da2126cb33391428ba0d6d10787f", - 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"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", + "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_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", + "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", + "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", + "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", + "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" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T13:40:29.820359" + "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 7343798f7..0c6816a59 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -15,176 +15,22 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, + { assert workflow.success}, { assert snapshot( - // These files are not stable - file("${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 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("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") - ).match("versions") } + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), + // All files with stable contents + stable_path + ).match() } ) } } @@ -203,21 +49,21 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, + { assert workflow.success}, { assert snapshot( - UTILS.removeNextflowVersion("$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("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // 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 b0ff0b3fb..764adab68 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -1,241 +1,345 @@ { - "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" + 35, + { + "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" + } + }, + [ + "bbsplit", + "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", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", + "fastqc", + "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", + "kallisto", + "kallisto/RAP1_IAA_30M_REP1", + "kallisto/RAP1_IAA_30M_REP1/abundance.h5", + "kallisto/RAP1_IAA_30M_REP1/abundance.tsv", + "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", + "kallisto/kallisto.merged.gene_counts.tsv", + "kallisto/kallisto.merged.gene_counts_length_scaled.SummarizedExperiment.rds", + "kallisto/kallisto.merged.gene_counts_length_scaled.tsv", + "kallisto/kallisto.merged.gene_counts_scaled.SummarizedExperiment.rds", + "kallisto/kallisto.merged.gene_counts_scaled.tsv", + "kallisto/kallisto.merged.gene_lengths.tsv", + "kallisto/kallisto.merged.gene_tpm.tsv", + "kallisto/kallisto.merged.transcript_counts.SummarizedExperiment.rds", + "kallisto/kallisto.merged.transcript_counts.tsv", + "kallisto/kallisto.merged.transcript_lengths.tsv", + "kallisto/kallisto.merged.transcript_tpm.tsv", + "kallisto/tx2gene.tsv", + "multiqc", + "multiqc/multiqc_report.html", + "multiqc/multiqc_report_data", + "multiqc/multiqc_report_data/cutadapt_filtered_reads_plot.txt", + "multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", + "multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "multiqc/multiqc_report_data/fastqc-status-check-heatmap.txt", + "multiqc/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", + "multiqc/multiqc_report_data/fastqc_per_base_n_content_plot.txt", + "multiqc/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/multiqc_report_data/fastqc_sequence_counts_plot.txt", + "multiqc/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", + "multiqc/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_report_data/kallisto_alignment.txt", + "multiqc/multiqc_report_data/multiqc_citations.txt", + "multiqc/multiqc_report_data/multiqc_cutadapt.txt", + "multiqc/multiqc_report_data/multiqc_data.json", + "multiqc/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt", + "multiqc/multiqc_report_data/multiqc_general_stats.txt", + "multiqc/multiqc_report_data/multiqc_kallisto.txt", + "multiqc/multiqc_report_data/multiqc_software_versions.txt", + "multiqc/multiqc_report_data/multiqc_sources.txt", + "multiqc/multiqc_report_plots", + "multiqc/multiqc_report_plots/pdf", + "multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf", + "multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", + "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", + "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/multiqc_report_plots/pdf/general_stats_table.pdf", + "multiqc/multiqc_report_plots/pdf/kallisto_alignment-cnt.pdf", + "multiqc/multiqc_report_plots/pdf/kallisto_alignment-pct.pdf", + "multiqc/multiqc_report_plots/png", + "multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png", + "multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png", + "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", + "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "multiqc/multiqc_report_plots/png/fastqc-status-check-heatmap.png", + "multiqc/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png", + "multiqc/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png", + "multiqc/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png", + "multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", + "multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", + "multiqc/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png", + "multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png", + "multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png", + "multiqc/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png", + "multiqc/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/multiqc_report_plots/png/general_stats_table.png", + "multiqc/multiqc_report_plots/png/kallisto_alignment-cnt.png", + "multiqc/multiqc_report_plots/png/kallisto_alignment-pct.png", + "multiqc/multiqc_report_plots/svg", + "multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", + "multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg", + "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", + "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", + "multiqc/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg", + "multiqc/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg", + "multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", + "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", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", + "trimgalore", + "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", + "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", + "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", + "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", + 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"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" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:53:37.272547" - }, - "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" - }, - 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"kallisto.merged.transcript_counts.tsv", - "kallisto.merged.transcript_lengths.tsv", - "kallisto.merged.transcript_tpm.tsv" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T15:53:37.166056" - }, - "references": { - "content": [ - "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", - "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T15:25:12.683541" - }, - "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=v3.15.1}}" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T15:35:31.742801" - }, - "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": "2024-08-23T15:25:12.695474" - }, - "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", - "kallisto_alignment-cnt.pdf", - "kallisto_alignment-pct.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", - "kallisto_alignment-cnt.png", - "kallisto_alignment-pct.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", - "kallisto_alignment-cnt.svg", - "kallisto_alignment-pct.svg" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T15:53:37.413284" - }, - "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": "2024-08-23T15:25:12.672876" + "timestamp": "2024-10-02T07:46:44.393695" }, "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}}", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", - "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" + 17, + { + "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" + } + }, + [ + "custom", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", + "fastqc", + "fastqc/trim", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_plots", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", + "trimgalore", + "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", + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:36:19.174739" + "timestamp": "2024-10-02T07:47:31.044439" } -} \ No newline at end of file +} diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy deleted file mode 100644 index 1bd58a496..000000000 --- a/tests/lib/UTILS.groovy +++ /dev/null @@ -1,11 +0,0 @@ -// Function to remove Nextflow version from pipeline_software_mqc_versions.yml - -class UTILS { - public static String removeNextflowVersion(pipeline_software_mqc_versions) { - def softwareVersions = path(pipeline_software_mqc_versions).yaml - if (softwareVersions.containsKey("Workflow")) { - softwareVersions.Workflow.remove("Nextflow") - } - return softwareVersions - } -} diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index dde1c3706..7ffef71de 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -13,797 +13,22 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${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, - 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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("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name - ).match("star_salmon/featurecounts") }, - { assert snapshot( - path("${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("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") - ).match("versions") } + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), + // All files with stable contents + stable_path + ).match() } ) } } @@ -820,31 +45,21 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.removeNextflowVersion("$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("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // 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 c82193e9d..1533ec60d 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -1,970 +1,1373 @@ { - "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" + 152, + { + "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" + } + }, + [ + "bbsplit", + "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", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", + "fastqc", + "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", + "multiqc/star_salmon", + "multiqc/star_salmon/multiqc_report.html", + "multiqc/star_salmon/multiqc_report_data", + "multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt", + "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt", + "multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_data.json", + "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_fail_mapped_samples_table.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt", + "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", + "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", + "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt", + "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt", + "multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt", + "multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt", + "multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt", + "multiqc/star_salmon/multiqc_report_data/salmon_plot.txt", + "multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt", + "multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt", + "multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt", + "multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt", + "multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt", + "multiqc/star_salmon/multiqc_report_data/star_summary_table.txt", + "multiqc/star_salmon/multiqc_report_plots", + "multiqc/star_salmon/multiqc_report_plots/pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fail_mapped_samples_table.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf", + 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"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" + 22, + { + "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" + } + }, + [ + "custom", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", + "fastqc", + "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", + "multiqc/star_salmon", + "multiqc/star_salmon/multiqc_data", + "multiqc/star_salmon/multiqc_plots", + "multiqc/star_salmon/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", + "trimgalore", + "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", + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T13:06:37.041504" + "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 430f18b6f..66084a8c9 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -13,923 +13,22 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${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("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name - ).match("star_salmon/dupradar") }, - { assert snapshot( - path("${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("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") - ).match("versions") } + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), + // All files with stable contents + stable_path + ).match() } ) } } @@ -946,31 +45,21 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.removeNextflowVersion("$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("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // 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 64a3f6c91..6097461ef 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -1,1102 +1,1623 @@ { - "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" + 205, + { + "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" + } + }, + [ + "bbsplit", + "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", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", + "fastqc", + "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", + "multiqc/star_salmon", + "multiqc/star_salmon/multiqc_report.html", + "multiqc/star_salmon/multiqc_report_data", + "multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt", + "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt", + "multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_data.json", + "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sortmerna.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt", + "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", + "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", + "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt", + "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt", + "multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt", + "multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt", + "multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt", + "multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt", + "multiqc/star_salmon/multiqc_report_data/salmon_plot.txt", + "multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt", + "multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt", + "multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt", + "multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt", + "multiqc/star_salmon/multiqc_report_data/sortmerna-detailed-plot.txt", + "multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt", + "multiqc/star_salmon/multiqc_report_data/star_summary_table.txt", + "multiqc/star_salmon/multiqc_report_plots", + "multiqc/star_salmon/multiqc_report_plots/pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf", + 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"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" + 24, + { + "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" + } + }, + [ + "custom", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", + "fastqc", + "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", + "multiqc/star_salmon", + "multiqc/star_salmon/multiqc_data", + "multiqc/star_salmon/multiqc_plots", + "multiqc/star_salmon/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", + "trimgalore", + "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", + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T13:19:36.107982" + "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 9105ed9fa..c0a386da0 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -15,216 +15,22 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, + { assert workflow.success}, { assert snapshot( - // These files are not stable - file("${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 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") } + // 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 + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), + // All files with stable contents + stable_path + ).match() } ) } } @@ -243,31 +49,21 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, + { assert workflow.success}, { assert snapshot( - UTILS.removeNextflowVersion("$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("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // 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 6ce551414..c528c6180 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -1,297 +1,418 @@ { - "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", - "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,f789abe663d4b4214f0ddeb413a7f150", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "fastqc_top_overrepresented_sequences_table.txt", - "multiqc_data.json", - "multiqc_general_stats.txt", - "multiqc_salmon.txt", - "multiqc_software_versions.txt", - "multiqc_sources.txt", - "salmon_plot.txt" + 34, + { + "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" + } + }, + [ + "bbsplit", + "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", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", + "fastqc", + "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/multiqc_report.html", + "multiqc/multiqc_report_data", + "multiqc/multiqc_report_data/cutadapt_filtered_reads_plot.txt", + "multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", + "multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "multiqc/multiqc_report_data/fastqc-status-check-heatmap.txt", + "multiqc/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", + "multiqc/multiqc_report_data/fastqc_per_base_n_content_plot.txt", + "multiqc/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/multiqc_report_data/fastqc_sequence_counts_plot.txt", + "multiqc/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", + "multiqc/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_report_data/multiqc_citations.txt", + "multiqc/multiqc_report_data/multiqc_cutadapt.txt", + "multiqc/multiqc_report_data/multiqc_data.json", + "multiqc/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt", + "multiqc/multiqc_report_data/multiqc_general_stats.txt", + "multiqc/multiqc_report_data/multiqc_salmon.txt", + "multiqc/multiqc_report_data/multiqc_software_versions.txt", + "multiqc/multiqc_report_data/multiqc_sources.txt", + "multiqc/multiqc_report_data/salmon_plot.txt", + "multiqc/multiqc_report_plots", + "multiqc/multiqc_report_plots/pdf", + "multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf", + "multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", + "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", + "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", + "multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", + 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- "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": "2024-10-02T08:10:56.056197" }, "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}}", - "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" + 16, + { + "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" + } + }, + [ + "custom", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", + "fastqc", + "fastqc/trim", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_plots", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", + "trimgalore", + "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", + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T10:25:58.654392" + "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 8fd703462..3c03631cc 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -13,472 +13,22 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${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("${params.outdir}/salmon/WT_REP2/quant.sf").name - ).match("salmon_quant") }, - { assert snapshot( - path("${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") } + { 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 + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), + // All files with stable contents + stable_path + ).match() } ) } } @@ -495,31 +45,21 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.removeNextflowVersion("$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("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // 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 7fcb8480a..ffb89c42c 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -1,596 +1,809 @@ { - "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", - 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"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" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T12:11:58.071145" + "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 e5b3aa080..5053e103f 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -13,818 +13,24 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${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 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") } + { 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 + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), + // All files with stable contents + stable_path + ).match() } ) } } - // STUB ARE CURRENTLY NOT POSSIBLE - } diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index d40a54446..775d007ea 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -1,943 +1,1384 @@ { - "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" + 193, + { + "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" + } + }, + [ + "bbsplit", + "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", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", + "fastqc", + "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", + "multiqc/star_salmon", + "multiqc/star_salmon/multiqc_report.html", + "multiqc/star_salmon/multiqc_report_data", + "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt", + "multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_data.json", + "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt", + "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", + "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", + "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt", + "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt", + "multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt", + "multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt", + 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"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=v3.15.1}}" - ], - "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": "2024-10-02T08:24:30.328195" } -} \ No newline at end of file +} diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 0f03bc6db..268a1fabb 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -13,864 +13,22 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot( - // These files are not stable - file("${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( - - 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("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name - ).match("trimgalore") }, - { assert snapshot( - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") - ).match("versions") } + { 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 + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // All stable path name, with a relative path + getRelativePath(stable_name, outputDir), + // All files with stable contents + stable_path + ).match() } ) } } @@ -887,31 +45,21 @@ nextflow_pipeline { } then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') assertAll( - { assert workflow.success }, - { assert snapshot( - UTILS.removeNextflowVersion("$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("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + // 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 db393113e..ebf025d71 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -1,1029 +1,1502 @@ { - "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" + 188, + { + "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" + } + }, + [ + "bbsplit", + "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", + "custom/out", + "custom/out/genome_gfp.fasta", + "custom/out/genome_gfp.gtf", + "fastqc", + "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", + "multiqc/star_rsem", + "multiqc/star_rsem/multiqc_report.html", + "multiqc/star_rsem/multiqc_report_data", + "multiqc/star_rsem/multiqc_report_data/cutadapt_filtered_reads_plot.txt", + "multiqc/star_rsem/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", + "multiqc/star_rsem/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc-status-check-heatmap-1.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc-status-check-heatmap.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_adapter_content_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_per_base_n_content_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_counts_plot-1.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_counts_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/star_rsem/multiqc_report_data/junction_saturation_known.txt", + "multiqc/star_rsem/multiqc_report_data/junction_saturation_novel.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_citations.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_cutadapt.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_data.json", + "multiqc/star_rsem/multiqc_report_data/multiqc_dupradar-section-plot.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_fail_strand_check_table.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_general_stats.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_picard_dups.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_rsem.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_bam_stat.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_infer_experiment.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_junction_annotation.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_read_distribution.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_salmon.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_samtools_flagstat.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_samtools_idxstats.txt", + 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"Workflow": { + "nf-core/rnaseq": "v3.16.0" + } + }, + [ + "custom", + "custom/out", + "custom/out/genome_transcriptome.fasta", + "custom/out/genome_transcriptome.gtf", + "fastqc", + "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", + "multiqc/star_rsem", + "multiqc/star_rsem/multiqc_data", + "multiqc/star_rsem/multiqc_plots", + "multiqc/star_rsem/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", + "trimgalore", + "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", + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T17:25:05.907994" + "timestamp": "2024-10-02T08:31:54.433237" } -} \ No newline at end of file +} diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml index 47e347670..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: @@ -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..e58d744b4 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]}) @@ -592,7 +597,7 @@ 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' @@ -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"