From 0c9a1728c35c21eedc5348bcda266dd0115d5e4d Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Fri, 27 Sep 2024 14:07:11 -0700 Subject: [PATCH 01/31] pbsv --- modules/nf-core/pbsv/environment.yml | 9 +++ modules/nf-core/pbsv/main.nf | 91 +++++++++++++++++++++++++ modules/nf-core/pbsv/meta.yml | 57 ++++++++++++++++ modules/nf-core/pbsv/tests/main.nf.test | 73 ++++++++++++++++++++ modules/nf-core/pbsv/tests/tags.yml | 2 + 5 files changed, 232 insertions(+) create mode 100644 modules/nf-core/pbsv/environment.yml create mode 100644 modules/nf-core/pbsv/main.nf create mode 100644 modules/nf-core/pbsv/meta.yml create mode 100644 modules/nf-core/pbsv/tests/main.nf.test create mode 100644 modules/nf-core/pbsv/tests/tags.yml diff --git a/modules/nf-core/pbsv/environment.yml b/modules/nf-core/pbsv/environment.yml new file mode 100644 index 00000000000..524f2c784a9 --- /dev/null +++ b/modules/nf-core/pbsv/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "pbsv" +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::pbsv=2.9.0" diff --git a/modules/nf-core/pbsv/main.nf b/modules/nf-core/pbsv/main.nf new file mode 100644 index 00000000000..bc01bb826be --- /dev/null +++ b/modules/nf-core/pbsv/main.nf @@ -0,0 +1,91 @@ +// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :) +// https://github.com/nf-core/modules/tree/master/modules/nf-core/ +// You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace: +// https://nf-co.re/join +// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters. +// All other parameters MUST be provided using the "task.ext" directive, see here: +// https://www.nextflow.io/docs/latest/process.html#ext +// where "task.ext" is a string. +// Any parameters that need to be evaluated in the context of a particular sample +// e.g. single-end/paired-end data MUST also be defined and evaluated appropriately. +// TODO nf-core: Software that can be piped together SHOULD be added to separate module files +// unless there is a run-time, storage advantage in implementing in this way +// e.g. it's ok to have a single module for bwa to output BAM instead of SAM: +// bwa mem | samtools view -B -T ref.fasta +// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty +// list (`[]`) instead of a file can be used to work around this issue. + +process PBSV { + tag "$meta.id" + label 'process_single' + + // TODO nf-core: List required Conda package(s). + // Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10"). + // For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems. + // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below. + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pbsv:2.9.0--h9ee0642_0': + 'biocontainers/pbsv:2.9.0--h9ee0642_0' }" + + input: + // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group" + // MUST be provided as an input via a Groovy Map called "meta". + // This information may not be required in some instances e.g. indexing reference genome files: + // https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf + // TODO nf-core: Where applicable please provide/convert compressed files as input/output + // e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc. + tuple val(meta), path(bam) + + output: + // TODO nf-core: Named file extensions MUST be emitted for ALL output channels + tuple val(meta), path("*.bam"), emit: bam + // TODO nf-core: List additional required output channels/values here + 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}" + // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10 + // If the software is unable to output a version number on the command-line then it can be manually specified + // e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf + // Each software used MUST provide the software name and version number in the YAML version file (versions.yml) + // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive + // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter + // using the Nextflow "task" variable e.g. "--threads $task.cpus" + // TODO nf-core: Please replace the example samtools command below with your module's command + // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;) + """ + samtools \\ + sort \\ + $args \\ + -@ $task.cpus \\ + -o ${prefix}.bam \\ + -T $prefix \\ + $bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pbsv: \$(samtools --version |& sed '1!d ; s/samtools //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + // TODO nf-core: A stub section should mimic the execution of the original module as best as possible + // Have a look at the following examples: + // Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63 + // Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54 + """ + touch ${prefix}.bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pbsv: \$(samtools --version |& sed '1!d ; s/samtools //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/pbsv/meta.yml b/modules/nf-core/pbsv/meta.yml new file mode 100644 index 00000000000..9c67b12ff1a --- /dev/null +++ b/modules/nf-core/pbsv/meta.yml @@ -0,0 +1,57 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "pbsv" +## TODO nf-core: Add a description of the module and list keywords +description: write your description here +keywords: + - sort + - example + - genomics +tools: + - "pbsv": + ## TODO nf-core: Add a description and other details for the software below + description: "pbsv - PacBio structural variant (SV) calling and analysis tools" + homepage: "None" + documentation: "None" + tool_dev_url: "None" + doi: "" + licence: ['BSD-3-clause-Clear'] + +## TODO nf-core: Add a description of all of the variables used as input +input: + # Only when we have meta + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + + ## TODO nf-core: Delete / customise this example input + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + +## TODO nf-core: Add a description of all of the variables used as output +output: + #Only when we have meta + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + ## TODO nf-core: Delete / customise this example output + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + +authors: + - "@tanyasarkjain" +maintainers: + - "@tanyasarkjain" diff --git a/modules/nf-core/pbsv/tests/main.nf.test b/modules/nf-core/pbsv/tests/main.nf.test new file mode 100644 index 00000000000..47a1abdb290 --- /dev/null +++ b/modules/nf-core/pbsv/tests/main.nf.test @@ -0,0 +1,73 @@ +// TODO nf-core: Once you have added the required tests, please run the following command to build this file: +// nf-core modules test pbsv +nextflow_process { + + name "Test Process PBSV" + script "../main.nf" + process "PBSV" + + tag "modules" + tag "modules_nfcore" + tag "pbsv" + + // TODO nf-core: Change the test name preferably indicating the test-data and file-format used + test("sarscov2 - bam") { + + // TODO nf-core: If you are created a test for a chained module + // (the module requires running more than one process to generate the required output) + // add the 'setup' method here. + // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules). + + when { + process { + """ + // TODO nf-core: define inputs of the process here. Example: + + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + //TODO nf-core: Add all required assertions to verify the test output. + // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples. + ) + } + + } + + // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix. + test("sarscov2 - bam - stub") { + + options "-stub" + + when { + process { + """ + // TODO nf-core: define inputs of the process here. Example: + + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + //TODO nf-core: Add all required assertions to verify the test output. + ) + } + + } + +} diff --git a/modules/nf-core/pbsv/tests/tags.yml b/modules/nf-core/pbsv/tests/tags.yml new file mode 100644 index 00000000000..59ab3754578 --- /dev/null +++ b/modules/nf-core/pbsv/tests/tags.yml @@ -0,0 +1,2 @@ +pbsv: + - "modules/nf-core/pbsv/**" From 5339e163dc4304567d5049f692cfb50fcd953b74 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 22 Oct 2024 07:22:04 +0000 Subject: [PATCH 02/31] [automated] Fix linting with Prettier --- modules/nf-core/pbsv/meta.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/pbsv/meta.yml b/modules/nf-core/pbsv/meta.yml index 9c67b12ff1a..6564ad89168 100644 --- a/modules/nf-core/pbsv/meta.yml +++ b/modules/nf-core/pbsv/meta.yml @@ -15,7 +15,7 @@ tools: documentation: "None" tool_dev_url: "None" doi: "" - licence: ['BSD-3-clause-Clear'] + licence: ["BSD-3-clause-Clear"] ## TODO nf-core: Add a description of all of the variables used as input input: @@ -25,7 +25,7 @@ input: description: | Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]` - + ## TODO nf-core: Delete / customise this example input - bam: type: file @@ -40,7 +40,7 @@ output: description: | Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]` - + - versions: type: file description: File containing software versions From dc0a3a1c700f00038e293c0a65c38e3254c479f1 Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Mon, 21 Oct 2024 17:27:50 -0700 Subject: [PATCH 03/31] version of pbsv module where all the tests pass --- modules/nf-core/pbsv/e1.fasta | 0 modules/nf-core/pbsv/environment.yml | 2 +- modules/nf-core/pbsv/main.nf | 22 ++++----- modules/nf-core/pbsv/tests/main.nf.test | 31 ++++++------- modules/nf-core/pbsv/tests/main.nf.test.snap | 49 ++++++++++++++++++++ 5 files changed, 73 insertions(+), 31 deletions(-) create mode 100644 modules/nf-core/pbsv/e1.fasta create mode 100644 modules/nf-core/pbsv/tests/main.nf.test.snap diff --git a/modules/nf-core/pbsv/e1.fasta b/modules/nf-core/pbsv/e1.fasta new file mode 100644 index 00000000000..e69de29bb2d diff --git a/modules/nf-core/pbsv/environment.yml b/modules/nf-core/pbsv/environment.yml index 524f2c784a9..cd84674e12f 100644 --- a/modules/nf-core/pbsv/environment.yml +++ b/modules/nf-core/pbsv/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::pbsv=2.9.0" + - "bioconda::pbsv" \ No newline at end of file diff --git a/modules/nf-core/pbsv/main.nf b/modules/nf-core/pbsv/main.nf index bc01bb826be..138191d16bd 100644 --- a/modules/nf-core/pbsv/main.nf +++ b/modules/nf-core/pbsv/main.nf @@ -1,7 +1,3 @@ -// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :) -// https://github.com/nf-core/modules/tree/master/modules/nf-core/ -// You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace: -// https://nf-co.re/join // TODO nf-core: A module file SHOULD only define input and output files as command-line parameters. // All other parameters MUST be provided using the "task.ext" directive, see here: // https://www.nextflow.io/docs/latest/process.html#ext @@ -36,10 +32,11 @@ process PBSV { // TODO nf-core: Where applicable please provide/convert compressed files as input/output // e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc. tuple val(meta), path(bam) + path(fasta) output: // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.bam"), emit: bam + tuple val(meta), path("*.vcf"), emit: vcf // TODO nf-core: List additional required output channels/values here path "versions.yml" , emit: versions @@ -59,17 +56,13 @@ process PBSV { // TODO nf-core: Please replace the example samtools command below with your module's command // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;) """ - samtools \\ - sort \\ - $args \\ - -@ $task.cpus \\ - -o ${prefix}.bam \\ - -T $prefix \\ - $bam + #pbmm2 align ${fasta} ${bam} ${prefix}.bam + pbsv discover ${bam} ${prefix}.svsig.gz + pbsv call -j 8 ${fasta} ${prefix}.svsig.gz ${prefix}.pbsv.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": - pbsv: \$(samtools --version |& sed '1!d ; s/samtools //') + pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //') END_VERSIONS """ @@ -82,10 +75,11 @@ process PBSV { // Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54 """ touch ${prefix}.bam + touch ${prefix}.pbsv.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": - pbsv: \$(samtools --version |& sed '1!d ; s/samtools //') + pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //') END_VERSIONS """ } diff --git a/modules/nf-core/pbsv/tests/main.nf.test b/modules/nf-core/pbsv/tests/main.nf.test index 47a1abdb290..cbf80381b19 100644 --- a/modules/nf-core/pbsv/tests/main.nf.test +++ b/modules/nf-core/pbsv/tests/main.nf.test @@ -10,14 +10,7 @@ nextflow_process { tag "modules_nfcore" tag "pbsv" - // TODO nf-core: Change the test name preferably indicating the test-data and file-format used - test("sarscov2 - bam") { - - // TODO nf-core: If you are created a test for a chained module - // (the module requires running more than one process to generate the required output) - // add the 'setup' method here. - // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules). - + test("pbsv_bam") { when { process { """ @@ -25,7 +18,11 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true) + ] + + input[1] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true) ] """ } @@ -34,16 +31,16 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } - //TODO nf-core: Add all required assertions to verify the test output. - // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples. + { assert snapshot(process.out.versions).match("versions") }, + { assert process.out.vcf != null }, + { assert file(process.out.vcf[0][1]).name == "test.pbsv.vcf" } ) } + } - // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix. - test("sarscov2 - bam - stub") { + test("pbsv_bam_stub") { options "-stub" @@ -54,8 +51,11 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true) ] + input[1] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true) + ] """ } } @@ -64,7 +64,6 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot(process.out).match() } - //TODO nf-core: Add all required assertions to verify the test output. ) } diff --git a/modules/nf-core/pbsv/tests/main.nf.test.snap b/modules/nf-core/pbsv/tests/main.nf.test.snap new file mode 100644 index 00000000000..475185d26e1 --- /dev/null +++ b/modules/nf-core/pbsv/tests/main.nf.test.snap @@ -0,0 +1,49 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,114b69a5e731b0691d6e523c12f7a8ca" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-21T17:23:23.323954" + }, + "pbsv_bam_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.pbsv.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,114b69a5e731b0691d6e523c12f7a8ca" + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test.pbsv.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,114b69a5e731b0691d6e523c12f7a8ca" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-21T17:25:35.357742" + } +} \ No newline at end of file From 71cab1d93bbbe0c684eb64cc4863c1dc7f7c7dcd Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Mon, 21 Oct 2024 17:39:02 -0700 Subject: [PATCH 04/31] getting rid of un-need comments --- modules/nf-core/pbsv/main.nf | 43 +------------------- modules/nf-core/pbsv/tests/main.nf.test.snap | 6 +-- 2 files changed, 5 insertions(+), 44 deletions(-) diff --git a/modules/nf-core/pbsv/main.nf b/modules/nf-core/pbsv/main.nf index 138191d16bd..afd85b22df7 100644 --- a/modules/nf-core/pbsv/main.nf +++ b/modules/nf-core/pbsv/main.nf @@ -1,43 +1,18 @@ -// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters. -// All other parameters MUST be provided using the "task.ext" directive, see here: -// https://www.nextflow.io/docs/latest/process.html#ext -// where "task.ext" is a string. -// Any parameters that need to be evaluated in the context of a particular sample -// e.g. single-end/paired-end data MUST also be defined and evaluated appropriately. -// TODO nf-core: Software that can be piped together SHOULD be added to separate module files -// unless there is a run-time, storage advantage in implementing in this way -// e.g. it's ok to have a single module for bwa to output BAM instead of SAM: -// bwa mem | samtools view -B -T ref.fasta -// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty -// list (`[]`) instead of a file can be used to work around this issue. - process PBSV { tag "$meta.id" label 'process_single' - // TODO nf-core: List required Conda package(s). - // Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10"). - // For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems. - // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pbsv:2.9.0--h9ee0642_0': 'biocontainers/pbsv:2.9.0--h9ee0642_0' }" input: - // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group" - // MUST be provided as an input via a Groovy Map called "meta". - // This information may not be required in some instances e.g. indexing reference genome files: - // https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf - // TODO nf-core: Where applicable please provide/convert compressed files as input/output - // e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc. tuple val(meta), path(bam) path(fasta) output: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels tuple val(meta), path("*.vcf"), emit: vcf - // TODO nf-core: List additional required output channels/values here path "versions.yml" , emit: versions when: @@ -46,19 +21,9 @@ process PBSV { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10 - // If the software is unable to output a version number on the command-line then it can be manually specified - // e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf - // Each software used MUST provide the software name and version number in the YAML version file (versions.yml) - // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive - // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter - // using the Nextflow "task" variable e.g. "--threads $task.cpus" - // TODO nf-core: Please replace the example samtools command below with your module's command - // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;) """ - #pbmm2 align ${fasta} ${bam} ${prefix}.bam pbsv discover ${bam} ${prefix}.svsig.gz - pbsv call -j 8 ${fasta} ${prefix}.svsig.gz ${prefix}.pbsv.vcf + pbsv call -j ${task.cpus} ${fasta} ${prefix}.svsig.gz ${prefix}.pbsv.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -69,16 +34,12 @@ process PBSV { stub: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - // TODO nf-core: A stub section should mimic the execution of the original module as best as possible - // Have a look at the following examples: - // Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63 - // Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54 """ touch ${prefix}.bam touch ${prefix}.pbsv.vcf cat <<-END_VERSIONS > versions.yml - "${task.process}": + "${task.process}": pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //') END_VERSIONS """ diff --git a/modules/nf-core/pbsv/tests/main.nf.test.snap b/modules/nf-core/pbsv/tests/main.nf.test.snap index 475185d26e1..4d73565e94e 100644 --- a/modules/nf-core/pbsv/tests/main.nf.test.snap +++ b/modules/nf-core/pbsv/tests/main.nf.test.snap @@ -24,7 +24,7 @@ ] ], "1": [ - "versions.yml:md5,114b69a5e731b0691d6e523c12f7a8ca" + "versions.yml:md5,78a8c3eb6a67916a463a6d1dfaa4fae4" ], "vcf": [ [ @@ -36,7 +36,7 @@ ] ], "versions": [ - "versions.yml:md5,114b69a5e731b0691d6e523c12f7a8ca" + "versions.yml:md5,78a8c3eb6a67916a463a6d1dfaa4fae4" ] } ], @@ -44,6 +44,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T17:25:35.357742" + "timestamp": "2024-10-21T17:34:55.61846" } } \ No newline at end of file From ec70173136339d831f97306e7549f7b70b6229d9 Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Tue, 22 Oct 2024 00:29:01 -0700 Subject: [PATCH 05/31] updated: --- modules/modules | 208 +++++++++++++++++++++ modules/nf-core/hiphase/environment.yml | 9 + modules/nf-core/hiphase/main.nf | 91 +++++++++ modules/nf-core/hiphase/meta.yml | 57 ++++++ modules/nf-core/hiphase/tests/main.nf.test | 73 ++++++++ modules/nf-core/hiphase/tests/tags.yml | 2 + modules/nf-core/humid/tests/main.nf.test | 4 +- modules/nf-core/pbmm2/environment.yml | 9 + modules/nf-core/pbmm2/main.nf | 86 +++++++++ modules/nf-core/pbmm2/meta.yml | 57 ++++++ modules/nf-core/pbmm2/tests/main.nf.test | 73 ++++++++ modules/nf-core/pbmm2/tests/tags.yml | 2 + modules/nf-core/pbsv/environment.yml | 4 +- modules/nf-core/pbsv/main.nf | 2 +- modules/nf-core/pbsv/meta.yml | 85 +++++---- modules/nf-core/pbsv/tests/main.nf.test | 12 +- 16 files changed, 718 insertions(+), 56 deletions(-) create mode 100644 modules/modules create mode 100644 modules/nf-core/hiphase/environment.yml create mode 100644 modules/nf-core/hiphase/main.nf create mode 100644 modules/nf-core/hiphase/meta.yml create mode 100644 modules/nf-core/hiphase/tests/main.nf.test create mode 100644 modules/nf-core/hiphase/tests/tags.yml create mode 100644 modules/nf-core/pbmm2/environment.yml create mode 100644 modules/nf-core/pbmm2/main.nf create mode 100644 modules/nf-core/pbmm2/meta.yml create mode 100644 modules/nf-core/pbmm2/tests/main.nf.test create mode 100644 modules/nf-core/pbmm2/tests/tags.yml diff --git a/modules/modules b/modules/modules new file mode 100644 index 00000000000..e8b417360df --- /dev/null +++ b/modules/modules @@ -0,0 +1,208 @@ +>chr19:45760000-45770300 +catgttggccaggctggtctccaactcctgacctcgagtgatccgcccac +cttggcctcctagagtgctgggattacaggtgtgagccaccgtgcccagc +Ttcccacatcattttacaactactctacgaagcagggtctcctgtggccc +cattttacagataaggaaattgaaatcaaaagactaagctgggcgcggtg +gctcacacctgtaatctcagcagtttgagaggctgacgtaggcggatcac +ctgagatcaggagttcaagaccagcctggccaacatggggaaaccccatt +tctactaaaaatacaagaaGTGTccgggcgtggtggctcacgcctgtaat +cccactattttgggaggccgaggagggcagatcacctgaggtcaggagtt +ggagaccaaccagtctggccatcatggcgaaatactatctctactaaaaa +tacaaaattagccgggtgtggtggtacgtgcctgtaatcccagctactca +ggaggctgaggcagaagaatcgcttaaacctgggaggcgggggttgcagt +aagccaagatggcaccgttggactgcagcctgggcaacaagagcgaaacc +cagtctcaaaaaaggaaaagaaaaagaaaaagaaaTTATCAGGGTGTggc +cgggcgtggtggctcatgcctatacttctagcactttgggaggctgaggc +gggcagatcacctgaggtcaggagtttaaacctagcttgaccaatatgat +gaaaccccctctctactaaaaatacaaaattagctgggcgtggtggtggg +cacttgtaaccccagttactcaggagtctgaggcaggagaatcacttgaa +cccaagaggtggagaatggagctgagatggtgccattgcactccagcctg +agggacaagagtaagactccgtctcaaaaaaaaaaaaaagaaagaaaaga +aaaaaaagaaaagaaaggaagaaagaaagaaagacagggtcttgctttgt +tgcccaggctggagtgcagtgtcaccatcatagatcagtgccttgaactc +ctgggctcaaatgaccctcccacaccaccatgcccagctggttttttaaa +ttatttttaaatttaacttaattcaatttctttttttttttttgagacag +agtctcactctgtcacccaggctggagtgcagtggtacgatctcggctca +ctgcaacctccgcctcctggatttaagcgattcttgtgcctcagcctcca +gagtagctgggactacaggcgcccaccaacatacctggctaattttttag +tatttttagacagagtttcgccatgttggccaggctggttttgaactcct +gacctcaggtgatcctcctgcctcagcctccgaaagtgctgagattacag +gcatgagccactgcgcctggccTAtttttttttttttttttttttttttt +ttgtagaacaaggtctctctatgttgcccaggctggtctgtaactcctgg +cctcaagcagtcctcctgcctcagcctcccagagtgttggggttacaggc +gtaagccaccacaccctgccAATCTGAGCTGCTGCTAATGCTCATGTTAT +GTCCTAGAAAAGCAGTACTGGGGGGATGAAGGGGCACCACTTGTCTCCCC +TCCCATCTTTCTCCCTCATCATGCCCCAGGACACAGCCTCCAAGGCCCCC +AAAGACCCTCCTGAGTCCCACAGCCTGCACCGGTCCTCAGTCTCGCTGGA +CCACTGCTACCTCTCGCTGAGCGGGAACAGCAAGGCGCCAtccagctcca +gctccagctccagctccagctccagctcGGAGGACAGCGACTCGGAGCCC +CTGTGGAAGCAGCGAGAGGTGAGAGACACGGCCGCATGCCAGGGCCAGCA +GGGCCTCCTTCCTCTCTCACCACCCTCTCCCTCCCCCAGGATATGCAGGC +CAACCCTGTGGGCACGCCGGGCTCCAGCGAAGAGGACGAAGACACCACAT +GGACCCCCACCCGGCTGGCCTCACCCCTGCTGGCAGCTGAGAAAAAGGCC +ACGAAGGGCCAAGTAGCCAGGGCCCCTGTGAAGCCCAAGGAGAAGAAGAA +AGGCCCCTGCCCACCCCAGATGAAGAAGAAGTGTGTCAACGGCTTCATCA +TGTTCTGCAGGATGAACCGGAAGCAGTACATCCGGTGGGTAGGGGGTCGT +CTTTGGCCCTGGGGAAGGCCCTGGCTTCGTTCTCTGCCCGCAGCCTGGCC +ATGCCGCTCCTCACAACTGTCTGACACTTTTTCCCCCTCCGAGACCCCAC +AAACCCTTCGTGGACCACAGTTCTTCCCCAGAACTGAACCCGGCCCCATt +gtattggacagggtccatccattgtcagcgctgaaacccaattcaggctt +tagacttcagaaaaaaaggagttttttttgttttgttttgttttttgaga +cagagtctcactctattgcccaggctgtagtgcagtggcacaatcacagc +tcactgcaatgtctgcctcccgggctcaaatcactgcaacctctgcctct +cagattctcctgcctcagcctcctgagtagctgggataacaggcgcgcca +tcagctaatttttgtatttttagtagagacagggtttcaccatgttggcc +aggctggtctcgaatgcctcacctcaagtgatctgcctgcctcggcctct +caaattgctgggattacaggtgtgagccatcaggcccagcaagaaaagaa +aatgaattggcttatataacctagaaaacaagggcgggtatagactgcct +tgagacatagctggttttagggctcacacaggctgtctggaatctttgtc +cttttcacccagttcctctgtcttccgggctggcttcattctctggcagg +tggggtcaccccaggaggcacaggctcgggtcctgtcccccacccaagcg +accccgggaggaggagaggtctctaaggttttaagcaaagtccttgggac +tgactttggtagatccggtgccaaccctgaaccagtcactgccaggCCTG +GAGCCAGGGGATGGGGAGGCCCCCCCCAAGCCACAGTGGAAAACAGCTAG +TTCCTTTACAGGAAGATCCAGATGTGGGGGCCAGGAGCGGTGCCCACAGG +TCCCCTGCACTCTCCTGGGACACCAGGTGCCCCCTTGTGAACAGCCGCTG +AGTCCAGCTCCCTCTGCCTCCTCAGCTCCAGAGGGTGGTCTTGGAGGCCT +TGTAGACCCACAAGGCTAGGAAGGGTCTGAGTTCTCAGTCAGGGTGTCCT +GCAGACCTCTCCTTACCTCCTCCTCCTTCCTGTCCCAGATCCTGCCCTGG +AACCGCTTCCACAGCTGCCACCAAGGAGCTGGCCCAGCTGTGGCGGGTGA +TGACCCAGCAGGAGCGGAGGCCATACTGGTGAGAGGCTCCGGCCCCGAGG +TGTGGGTGGGGGGTGGAAGAGCCTCCCTACCCCGGAACCCTGCTCTGTCT +CTGGAGCCTTGGGTGTCATGGCATGGGAGACTGGGCCGAGGAATTTGCGT +GTTGCCCCTTCTTATGAAACCCTTGGGGGTGACACAGGTGTAGGGGTACC +CCACCACAGCTAAGCTGGGGAACAGCTGAGCCCAGACATGGACCCCTGCC +TCAATTCTTTTGCTGTCTCTGCCACACGACTTTCTCGGGGCGTGGTCTGA +TTTTCCTGTCGCTTGGCCACCTCGACTCCCCCGAATCCTGTCCCCTCCAC +CTTCAAGGAGCTGCCACCTGCCCTGGCTCCTGACTTTGAACACATCCCAG +AGCCCTTGGCCGAGTCCCATCTTACTGACTGGGACTTGGTGGACCCAAGG +CTCGCCCAATAGAGGCTAAAACGGTGGCCCAGGCCCCTGCGGGGACACAG +GATTGGGAGTGGTACAGGGATGCCCGGGAGGCGAGTGAGGAAGCCAGGCC +ATCCTGCCACCGTCTCCCCAGCACCAAGGCTCGCAGGTTCAGCCGCCAGC +ACAACCGCATCGTGAAGCAGGACGGCTCCAGCAGCGAGGCTGAGGACTGG +GAGACGCCAAAGCCCTTCTACCAGCTGCTGGCCGAGAAGGCCTTGCCGCT +GCCCCCGCACCTCCAGTGAGAGGGCGGCCCCTCGCCTCGCTCCCCTCACC +CCTCATGGCAACCGCGGCTCTTGCTGGAAGCCAGGACCCATCGATGAACT +TGTCCCTCCTGGGCCTCCAGCCCCTGAGAATGCAGGTCCCATGGGACTGG +GGAGGGGGGCACTGATTAGCCCCAACCGCTGGGCACATTTGCCTGGAGCA +CCAGAGTCACCCACAGCTGCCTTGATTCTCCCCCAGGCTTAGGAAGGAAA +CCCAAAATGAAATGCGGGGTGTCGGAAGGTGAAGTTTACCCACCCCTCTC +CCCTTCCCTTCCCCACCCCAGAGCCACTCGGTTGCAACCCTGTTCATGCT +CACCTCACCCTACTCCTCCCTCTCCTGTTCTATTTTTAGACTATTTATTG +TTTTAAATAAAATAAAGCAAGTGGAACCTTTGTTACCAGCAAGAGAGACA +AGGGCAGGCCCTCCTGCGTCCCCCTGCTGCCCCACTGGGGTGCTCCGTCC +ACCCTCATCTGGAGGCCTGTGGCTTGCAAGAGGCCTCAGTGCCACCCCCT +CCCCAGCCACTCTGTGCATCTGAATGCAAACCCCTCTTCCCCTCGGGAGG +CAGCAATGGGAAGGCCAGGTCTCGAGGTGGGCTCTGTGTTCAGCGCTGCT +TTGGACAGACACTGGAAGGCACCCCAGACCCCTGGTGGTGGTGTAATCCG +ATAACTTTATTTTAATTGAAAATGGAGGCATAACATGTCCTAGAAAAATA +AAGATTTAGGATACAAAGGAGACACAGCGGCAGGGCTGCCCCCAGGGATG +AGGGAATCTTTGGTCTGGGCCGGATAATGAGGACAAGGGCTTGAGTCGAG +GGGAGCTGGTGAAGGAAGACCCCCGTCTCCCCACAGCTGCCCCACCCCCC +GCCCCTGGCAGGAAATGCCACACTGGGGAGGGTCTCCAGTCTCAGGGGCG +CGGGGCTGCCTGTCCTCCACCTTCGGATTCCAGGCAGTTGTGACAACACC +AGCTATCGGCAGAGCTATTAATAGTGTTTCAGGGAGTGACAGGGAGAGGG 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+GGAGGAAGTTTCCTGTGGGGAGAGAGGGACCGAGCGCAGGTGAGAGCCAG +GAGAGCAGGCCAAGCCAGAGAGAAGTGGAGACTGTGCAGCTGGAGGGCGG +GCGGAGGGAGCCTTGTGGTGGGCCTTGGGGCACTGGGACTTGCCAGGGAT +GAGATGCCCTCCAGGAGCCCAGGGACAGCCCCTCCCTCTCCGAGATGACT +GCACCCCTCCCCGGCTCTCACCTAGGCCTGAGGGAGGGAGATGGGGGTAC +CTGGGGCAGTGGCCGAAGGCAGCTGCAGGGCAGTCACGCCCACCCCGGAG +TTGATGAGGTGCACATTGGCAGGGCCTGCTGCAGCTGCCACCTTCACAGG +GCTGCCTGGCCCGGCTGCCAACAGCTGCAGGGGCCCCACAGCCTGGGGCA +GGGTCACCACCTGTGAGGTGGGTACTACCTGGGGCAGGTTCAATAGTGGG +GAGGTGGGGCTCAGGCCCGTGGGATACCCCGGGGGTGGGGAGAGCGGTAC +CACTTGTGGGGCAGCCACAGCAGGCACTGGCCCCGGGGGCAGAGGAAAGG +TGGCAGCCGTCGGGGGGCCAGGCACCACTTGGGCCAGGGGCCCCAGGACC +TCCTCTCCAAGGGCTGGTCCCGGAGCAGCCACCTGGGCCCCTTTGGTCTC +AGGGGCCTCCGACTGAGCCTCCTCCAGCCGCACCTCCCCTGTCTGAGGGT +CCAGGACCAGAGAGGTCTTGGTCTCGCTGGCCCCCTGAGGGCTGGGCTGC +GGTGGAGGGGCACCCCCGCCCCCAGTGAGCAGCAGCGGGCCCAGGCTGGA +GGCCTCGCCCAGGGCCAGGCCGTTGATGATGACGGGGCCCCCGTTGAGGA +GCACTGCTGGGGAGCCGCTGGCTGCCAGGAAGCTCCCGTTCACCAGGATG +GAGGAGGAAGCCGGGCAAGGCGCGGGAGGGCCGGTCCCTGCCAGGAATAT +GGAGCCCTGGGCAGCGGCCTCGGCGGACACTGGGGCCGCCCCTCTCTCCA +GGTCCTCAGGACTTCGGCTGGACTCGTCCTCAGTCGTGGGATTCCCATCA +GACTCGCTGGCCGGAGAAATGGCTGTCAGCTGGGGTCCCTTAGCCTGTGG +GGCCTCCCGCATAGCCAGCCAGCTGCTCCCCCACCTTTCCCTGGCCCAAG +TTTCGGTGGATCATTCCAGGGGTTATGACGCCTCTCTGAGACCACTCCAA +ACTCCAGGGCCTTTTGCAAGCCCTGCGTGGACACCACTGCAGAGAAGCGC +TGGGGAGGGAAGAGGCCCTTGCTCTCCCCCACCTCGGCCTCGGGTCCCCA +GAGGCTGAGCTCCCAGGTTGCCCTAAAAGTTCCTTGGTTGGGCGGAAAGC +GGGCGAGTGGCCTGGAGAGAGGGAGCAGCAGCCGCCAGCCCAGTTCCCGG +TGCCCTCCCCGCGGGGCGTCAGAGAAGGGAGAGGCCGGCGCTCAGGGTGG +GAGGAGAAGGGTTTGGGTTACAGGGAAACCGGAGCTGGGAAAGGTTCACG +TTTCACAACAAAGGCAGAAGACGGACCACGCCGTCCGGGCCCGGAGGGAG +TGTGGGGGCGGGTGGGTAAGAGTAACGGTCAGTGAAGAAAGGGGGCTGGG +AGGCAGCCCCTACGCGGAGTGGAGTGGCCACAGGCCCTGTCCTTTTTCCT +CAGTCCCTCTAGTGCCCCCCGCAGTGTGATTCCCCAACACCGATGGGATT +TGGGAAGGAGCTCGGAATGGAGCCGCTGGAAGAGGAGACGCGTGCGGGGA +GAGGGCCCGGGCGGGTGCCTGTCCCGTCCACACTTAGTCCCCGCGCCCCG +CGGGCGCCTGAGATTGTGAGCTGGTCCCGGGAGATGTCCGAGGACCTCGG +CGCGCCGGCCCCAGCAGTGGGCACGGGGGAAGAGGGCTGGTGGACGGGAT +GTCCCCGGGAGAGCTGGACTTGCGCCGCCCGAGGCCCCTCACCTCTTGCA +GGGCGCGCCGCCTCCGGCCCCGGTCCGGTCGCGCTGTCGCCGGTTCTTGA +ACCAGTTGCTGACCTGCGTGAGCGACAGGCCGGTGAGTGTGGCCAGGCGG +CGCTTCTCGTCCGGCGTGGGGTAGCGGTTGCCGCGGTAGCAGGCCTTGAG +CGCTGCGCGGGAGCGCTCCTTGAAGCAGTAGACTGTCTCCTCGCCGTCCC +AGATGGTCTTGGGCAGCGGGAACTTCTTGCGCAGTCGATACTTGTCCACT +GCGCCAAGCGCGCGGCCGCGGGCCCGCTCGGCCTCATGGTAGCGCGCGCG +CAGGTAGAGGTCCTGCAGGAAGGCGTGGTGGGCGGCGGGGAAGGGGCGGC +TCTCGAGTAGCCGGTAGAGCTCGGCGTACTCGCCCCGCTGGAAGGCCACC +AGGGCCCGCGCGCGCAACACCGGGTCGCTGCCACGTAGGCGCTCGGCCGG +GGGCAGTGCGCCCAGGAAGCGGCTCAAGCGGCCGGCGTGGCCCGCCTGGA +GCAGCGCCTCGCAGACGCACGCCACCTGCTCGGGCGAGAAGCGGAGGCCC +GTGGGCGGTTCGGAAGCGGCCTCGGGGGGCGACCCGGGGACGCCCGGGGA +TCCCGGGCCCTCAGCTCCCGCAGCCGCTGCGCCCGCCCCGGCCCCGGCCG +CCGCCGCCGCCTCACCCTCGGCCGCCTGCAAAGTCTGCAAGAGCTGGCGC +GCTTCCTCCTCCTCCTCTTCGGTCGCCGCCGCCGCCGCCACCGCCTCCCC +CCCAGCCGCCGGCCCCGCGCTCGGCTCCGCAGGCAAGGTAGCCATGTTTT +GCAACTTTGGGAAGTTcctccctccctctcttcctccctcGGGCTTTCCC +CAGCCTCCTCCCCCACCTGTCCCCCCTTTTCGCCCCCACTCCCCGCTCTT +CTCGATCTTCTTTCTGGCCGACCCTGCGCCCCACGCCGGGAAGGCGAGAT +CCAGCTCTCCACTCGGGTCTCTGTCCCCTTGTGTGTGTCCGTCCCCCTCC +CGTCTGTCTGTGATTCTCCCTTTGTTTTCCCTCCGCCTCTGGCCGCGCTT +TCTGCCTCCCCCCAGCGTGTGCTTCTGGCTCAGGGCCTCAGTTTCCCCAT +CGGGACAACGCAGAAGGTAACGGGCCGTCCAGGAGGACTAAGGGCGCGAA +GCCTCCGCCCCGAGACTGAGCTTCTGCACGCCTCCGTCTCCAGGGTCCTC +TGCAGGCCCCCACATTCCCCATCTCGGCCTGCGCTCCGCCCCTCGGAATT +CCCGGCTCCGCAGGGGGGGCGGGTCTGGCCGGGAGGAGGGGCGGGGAACG +GGCTAGAAAGTTTGCAGCAACTTTTCTCGAGCTTGCGTCCCAGGAGCGGA +TGCGCGTGGCGTGCGCAGGCGCAGTGGAAGGAGGATGGCCGCGCGCGCTG +CCAGCCCAGCCCCCTCTTCTCGACGCTCGGTGGCACAGCTGGGCCACAGC +TGGGCGGGGGCGGTGCCTCCGGGTGGCCCGCTCGCCCTCCTATTGGCCGG +ACGCCAAAGCCCCGCCCCGTGGCTTTTCCTCCCCCAACCCTGATTCGGCC +GCTTCGCATCCCGCTAGCTCCTCCCAGACCTTCGGCCGCCTCCACACGCC +TCCGGATTGGCCCGCTGCGGAGCCTCCGGCCCACAACGCAAACCGCGGAC +ACTGTGGAGTCCAGAGCTTTGGGCAGATGGAGGGCCTTTTATTCGCGAGG +GTCGGGGGTGGGGGTCCTAGGTGGGGACAGACAATAAATACCGAGGAATG +TCGGGGTCTCAGTGCATCCAAAACGTGGATTGGGGTTGTTGGGGGTCCTG +TAGCCTGTCAGCGAGTCGGAGGACGAGGTCAATAAATATCCAAACCGCCG +AAGCGGGCGGAGCCGGCTGGGGCTCCGAGAGCAGCGCAAGTGAGGAGGGG +GGCGCGGGATCCCCGAAAAAGCGGGTTTGGCAAAAGCAAATTTCCCGAGT +AAGCAGGCAGAGATCGCGCCAGACGCTCCCCAGAGCAGGGCGTCATGCAC +AAGAAAGCTTTGCACTTTGCGAACCAACGATAGGTGGGGGTGCGTGGAGG +ATGGAACACGGACGGCCCGGCTTGCTGCCTTCCCAGGCCTGCAGTTTGCC +CATCCACGTCAGGGCCTCAGCCTGGCCGAAAGAAAGAAATGGTCTGTGAT +CCCCCcagcagcagcagcagcagcagcagcagcagcagcagcagcagcag +cagcagcagcagcagcaTTCCCGGCTACAAGGACCCTTCGAgccccgttc +g diff --git a/modules/nf-core/hiphase/environment.yml b/modules/nf-core/hiphase/environment.yml new file mode 100644 index 00000000000..cc1b89cdd7c --- /dev/null +++ b/modules/nf-core/hiphase/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "hiphase" +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::hiphase=1.4.5" diff --git a/modules/nf-core/hiphase/main.nf b/modules/nf-core/hiphase/main.nf new file mode 100644 index 00000000000..a1ddf21eb58 --- /dev/null +++ b/modules/nf-core/hiphase/main.nf @@ -0,0 +1,91 @@ +// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :) +// https://github.com/nf-core/modules/tree/master/modules/nf-core/ +// You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace: +// https://nf-co.re/join +// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters. +// All other parameters MUST be provided using the "task.ext" directive, see here: +// https://www.nextflow.io/docs/latest/process.html#ext +// where "task.ext" is a string. +// Any parameters that need to be evaluated in the context of a particular sample +// e.g. single-end/paired-end data MUST also be defined and evaluated appropriately. +// TODO nf-core: Software that can be piped together SHOULD be added to separate module files +// unless there is a run-time, storage advantage in implementing in this way +// e.g. it's ok to have a single module for bwa to output BAM instead of SAM: +// bwa mem | samtools view -B -T ref.fasta +// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty +// list (`[]`) instead of a file can be used to work around this issue. + +process HIPHASE { + tag "$meta.id" + label 'process_single' + + // TODO nf-core: List required Conda package(s). + // Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10"). + // For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems. + // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below. + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/hiphase:1.4.5--h9ee0642_0': + 'biocontainers/hiphase:1.4.5--h9ee0642_0' }" + + input: + // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group" + // MUST be provided as an input via a Groovy Map called "meta". + // This information may not be required in some instances e.g. indexing reference genome files: + // https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf + // TODO nf-core: Where applicable please provide/convert compressed files as input/output + // e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc. + tuple val(meta), path(bam) + + output: + // TODO nf-core: Named file extensions MUST be emitted for ALL output channels + tuple val(meta), path("*.bam"), emit: bam + // TODO nf-core: List additional required output channels/values here + 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}" + // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10 + // If the software is unable to output a version number on the command-line then it can be manually specified + // e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf + // Each software used MUST provide the software name and version number in the YAML version file (versions.yml) + // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive + // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter + // using the Nextflow "task" variable e.g. "--threads $task.cpus" + // TODO nf-core: Please replace the example samtools command below with your module's command + // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;) + """ + samtools \\ + sort \\ + $args \\ + -@ $task.cpus \\ + -o ${prefix}.bam \\ + -T $prefix \\ + $bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + hiphase: \$(samtools --version |& sed '1!d ; s/samtools //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + // TODO nf-core: A stub section should mimic the execution of the original module as best as possible + // Have a look at the following examples: + // Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63 + // Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54 + """ + touch ${prefix}.bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + hiphase: \$(samtools --version |& sed '1!d ; s/samtools //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/hiphase/meta.yml b/modules/nf-core/hiphase/meta.yml new file mode 100644 index 00000000000..f0df5dfec51 --- /dev/null +++ b/modules/nf-core/hiphase/meta.yml @@ -0,0 +1,57 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "hiphase" +## TODO nf-core: Add a description of the module and list keywords +description: write your description here +keywords: + - sort + - example + - genomics +tools: + - "hiphase": + ## TODO nf-core: Add a description and other details for the software below + description: "Small and structural variant phasing tool for PacBio HiFi reads" + homepage: "None" + documentation: "None" + tool_dev_url: "None" + doi: "" + licence: ['BSD-3-clause-Clear'] + +## TODO nf-core: Add a description of all of the variables used as input +input: + # Only when we have meta + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + + ## TODO nf-core: Delete / customise this example input + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + +## TODO nf-core: Add a description of all of the variables used as output +output: + #Only when we have meta + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + ## TODO nf-core: Delete / customise this example output + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + +authors: + - "@tanyasarkjain" +maintainers: + - "@tanyasarkjain" diff --git a/modules/nf-core/hiphase/tests/main.nf.test b/modules/nf-core/hiphase/tests/main.nf.test new file mode 100644 index 00000000000..f5fa06cda68 --- /dev/null +++ b/modules/nf-core/hiphase/tests/main.nf.test @@ -0,0 +1,73 @@ +// TODO nf-core: Once you have added the required tests, please run the following command to build this file: +// nf-core modules test hiphase +nextflow_process { + + name "Test Process HIPHASE" + script "../main.nf" + process "HIPHASE" + + tag "modules" + tag "modules_nfcore" + tag "hiphase" + + // TODO nf-core: Change the test name preferably indicating the test-data and file-format used + test("sarscov2 - bam") { + + // TODO nf-core: If you are created a test for a chained module + // (the module requires running more than one process to generate the required output) + // add the 'setup' method here. + // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules). + + when { + process { + """ + // TODO nf-core: define inputs of the process here. Example: + + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + //TODO nf-core: Add all required assertions to verify the test output. + // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples. + ) + } + + } + + // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix. + test("sarscov2 - bam - stub") { + + options "-stub" + + when { + process { + """ + // TODO nf-core: define inputs of the process here. Example: + + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + //TODO nf-core: Add all required assertions to verify the test output. + ) + } + + } + +} diff --git a/modules/nf-core/hiphase/tests/tags.yml b/modules/nf-core/hiphase/tests/tags.yml new file mode 100644 index 00000000000..33a31bb1dc0 --- /dev/null +++ b/modules/nf-core/hiphase/tests/tags.yml @@ -0,0 +1,2 @@ +hiphase: + - "modules/nf-core/hiphase/**" diff --git a/modules/nf-core/humid/tests/main.nf.test b/modules/nf-core/humid/tests/main.nf.test index 987bc20cc03..3d0b839ac1e 100644 --- a/modules/nf-core/humid/tests/main.nf.test +++ b/modules/nf-core/humid/tests/main.nf.test @@ -77,7 +77,9 @@ nextflow_process { { assert snapshot(process.out.log, process.out.stats, process.out.versions).match()}, - {assert file(process.out.dedup[0][1].find { + { + println process.out.dedup[0][1] + assert file(process.out.dedup[0][1].find { file(it).name == "test_1_dedup.fastq.gz" }).exists()}, {assert file(process.out.dedup[0][1].find { file(it).name == "test_2_dedup.fastq.gz" }).exists()}, diff --git a/modules/nf-core/pbmm2/environment.yml b/modules/nf-core/pbmm2/environment.yml new file mode 100644 index 00000000000..ccddb46fed5 --- /dev/null +++ b/modules/nf-core/pbmm2/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "pbmm2" +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::pbmm2=1.14.99" diff --git a/modules/nf-core/pbmm2/main.nf b/modules/nf-core/pbmm2/main.nf new file mode 100644 index 00000000000..685262719f0 --- /dev/null +++ b/modules/nf-core/pbmm2/main.nf @@ -0,0 +1,86 @@ +// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :) +// https://github.com/nf-core/modules/tree/master/modules/nf-core/ +// You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace: +// https://nf-co.re/join +// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters. +// All other parameters MUST be provided using the "task.ext" directive, see here: +// https://www.nextflow.io/docs/latest/process.html#ext +// where "task.ext" is a string. +// Any parameters that need to be evaluated in the context of a particular sample +// e.g. single-end/paired-end data MUST also be defined and evaluated appropriately. +// TODO nf-core: Software that can be piped together SHOULD be added to separate module files +// unless there is a run-time, storage advantage in implementing in this way +// e.g. it's ok to have a single module for bwa to output BAM instead of SAM: +// bwa mem | samtools view -B -T ref.fasta +// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty +// list (`[]`) instead of a file can be used to work around this issue. + +process PBMM2 { + tag "$meta.id" + label 'process_single' + + // TODO nf-core: List required Conda package(s). + // Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10"). + // For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems. + // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below. + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pbmm2:1.14.99--h9ee0642_0': + 'biocontainers/pbmm2:1.14.99--h9ee0642_0' }" + + input: + // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group" + // MUST be provided as an input via a Groovy Map called "meta". + // This information may not be required in some instances e.g. indexing reference genome files: + // https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf + // TODO nf-core: Where applicable please provide/convert compressed files as input/output + // e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc. + tuple val(meta), path(bam) + tuple val(meta), path(fasta) + + output: + // TODO nf-core: Named file extensions MUST be emitted for ALL output channels + tuple val(meta), path("*.bam"), emit: bam + // TODO nf-core: List additional required output channels/values here + 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}" + // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10 + // If the software is unable to output a version number on the command-line then it can be manually specified + // e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf + // Each software used MUST provide the software name and version number in the YAML version file (versions.yml) + // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive + // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter + // using the Nextflow "task" variable e.g. "--threads $task.cpus" + // TODO nf-core: Please replace the example samtools command below with your module's command + // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;) + """ + pbmm2 align $fasta \${bam} \${bam} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pbmm2: \$(samtools --version |& sed '1!d ; s/samtools //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + // TODO nf-core: A stub section should mimic the execution of the original module as best as possible + // Have a look at the following examples: + // Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63 + // Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54 + """ + touch ${prefix}.bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pbmm2: \$(samtools --version |& sed '1!d ; s/samtools //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/pbmm2/meta.yml b/modules/nf-core/pbmm2/meta.yml new file mode 100644 index 00000000000..891060201f9 --- /dev/null +++ b/modules/nf-core/pbmm2/meta.yml @@ -0,0 +1,57 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "pbmm2" +## TODO nf-core: Add a description of the module and list keywords +description: write your description here +keywords: + - sort + - example + - genomics +tools: + - "pbmm2": + ## TODO nf-core: Add a description and other details for the software below + description: "A minimap2 frontend for PacBio native data formats" + homepage: "None" + documentation: "None" + tool_dev_url: "None" + doi: "" + licence: ['BSD-3-clause-Clear'] + +## TODO nf-core: Add a description of all of the variables used as input +input: + # Only when we have meta + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + + ## TODO nf-core: Delete / customise this example input + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + +## TODO nf-core: Add a description of all of the variables used as output +output: + #Only when we have meta + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + ## TODO nf-core: Delete / customise this example output + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + +authors: + - "@tanyasarkjain" +maintainers: + - "@tanyasarkjain" diff --git a/modules/nf-core/pbmm2/tests/main.nf.test b/modules/nf-core/pbmm2/tests/main.nf.test new file mode 100644 index 00000000000..2c382a75601 --- /dev/null +++ b/modules/nf-core/pbmm2/tests/main.nf.test @@ -0,0 +1,73 @@ +// TODO nf-core: Once you have added the required tests, please run the following command to build this file: +// nf-core modules test pbmm2 +nextflow_process { + + name "Test Process PBMM2" + script "../main.nf" + process "PBMM2" + + tag "modules" + tag "modules_nfcore" + tag "pbmm2" + + // TODO nf-core: Change the test name preferably indicating the test-data and file-format used + test("pbmm2 - bam") { + + // TODO nf-core: If you are created a test for a chained module + // (the module requires running more than one process to generate the required output) + // add the 'setup' method here. + // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules). + + when { + process { + """ + // TODO nf-core: define inputs of the process here. Example: + + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + //TODO nf-core: Add all required assertions to verify the test output. + // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples. + ) + } + + } + + // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix. + test("sarscov2 - bam - stub") { + + options "-stub" + + when { + process { + """ + // TODO nf-core: define inputs of the process here. Example: + + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + //TODO nf-core: Add all required assertions to verify the test output. + ) + } + + } + +} diff --git a/modules/nf-core/pbmm2/tests/tags.yml b/modules/nf-core/pbmm2/tests/tags.yml new file mode 100644 index 00000000000..2472daa0786 --- /dev/null +++ b/modules/nf-core/pbmm2/tests/tags.yml @@ -0,0 +1,2 @@ +pbmm2: + - "modules/nf-core/pbmm2/**" diff --git a/modules/nf-core/pbsv/environment.yml b/modules/nf-core/pbsv/environment.yml index cd84674e12f..0bd59695b49 100644 --- a/modules/nf-core/pbsv/environment.yml +++ b/modules/nf-core/pbsv/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "pbsv" channels: - conda-forge - bioconda - - defaults dependencies: - - "bioconda::pbsv" \ No newline at end of file + - "bioconda::pbsv=2.9.0" \ No newline at end of file diff --git a/modules/nf-core/pbsv/main.nf b/modules/nf-core/pbsv/main.nf index afd85b22df7..0a103ccbf97 100644 --- a/modules/nf-core/pbsv/main.nf +++ b/modules/nf-core/pbsv/main.nf @@ -9,7 +9,7 @@ process PBSV { input: tuple val(meta), path(bam) - path(fasta) + tuple val(meta2), path(fasta) output: tuple val(meta), path("*.vcf"), emit: vcf diff --git a/modules/nf-core/pbsv/meta.yml b/modules/nf-core/pbsv/meta.yml index 6564ad89168..1d12c9bdc9c 100644 --- a/modules/nf-core/pbsv/meta.yml +++ b/modules/nf-core/pbsv/meta.yml @@ -1,56 +1,55 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "pbsv" -## TODO nf-core: Add a description of the module and list keywords -description: write your description here +description: Pacbio Structural Variant Caller in reads keywords: - - sort - - example - - genomics + - structural variants + - long-read analysis + - sequence analysis tools: - "pbsv": - ## TODO nf-core: Add a description and other details for the software below description: "pbsv - PacBio structural variant (SV) calling and analysis tools" - homepage: "None" - documentation: "None" - tool_dev_url: "None" - doi: "" + homepage: "https://github.com/tanyasarkjain/modules/tree/pbsv" + documentation: "https://github.com/tanyasarkjain/modules/tree/pbsv" + tool_dev_url: "https://github.com/tanyasarkjain/modules/tree/pbsv" licence: ["BSD-3-clause-Clear"] - -## TODO nf-core: Add a description of all of the variables used as input + identifier: "" input: - # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - ## TODO nf-core: Delete / customise this example input - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - -## TODO nf-core: Add a description of all of the variables used as output + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: "A BAM file containing an aligned reads" + pattern: "*.bam" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: Fasta file output: - #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - + - vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + pattern: "*.vcf.gz" + - "*.vcf": + type: file + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + pattern: "*.vcf.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - ## TODO nf-core: Delete / customise this example output - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tanyasarkjain" maintainers: diff --git a/modules/nf-core/pbsv/tests/main.nf.test b/modules/nf-core/pbsv/tests/main.nf.test index cbf80381b19..5f421f110cf 100644 --- a/modules/nf-core/pbsv/tests/main.nf.test +++ b/modules/nf-core/pbsv/tests/main.nf.test @@ -1,5 +1,3 @@ -// TODO nf-core: Once you have added the required tests, please run the following command to build this file: -// nf-core modules test pbsv nextflow_process { name "Test Process PBSV" @@ -13,15 +11,14 @@ nextflow_process { test("pbsv_bam") { when { process { - """ - // TODO nf-core: define inputs of the process here. Example: - + """ input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true) ] input[1] = [ + [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true) ] """ @@ -46,14 +43,13 @@ nextflow_process { when { process { - """ - // TODO nf-core: define inputs of the process here. Example: - + """ input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true) ] input[1] = [ + [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true) ] """ From e6ffe06ac128e1482c222ad628ca1047bae9b3b1 Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Tue, 22 Oct 2024 00:06:22 -0700 Subject: [PATCH 06/31] changed website: --- modules/nf-core/pbsv/meta.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/pbsv/meta.yml b/modules/nf-core/pbsv/meta.yml index 1d12c9bdc9c..f17cae43c98 100644 --- a/modules/nf-core/pbsv/meta.yml +++ b/modules/nf-core/pbsv/meta.yml @@ -8,9 +8,9 @@ keywords: tools: - "pbsv": description: "pbsv - PacBio structural variant (SV) calling and analysis tools" - homepage: "https://github.com/tanyasarkjain/modules/tree/pbsv" - documentation: "https://github.com/tanyasarkjain/modules/tree/pbsv" - tool_dev_url: "https://github.com/tanyasarkjain/modules/tree/pbsv" + homepage: "https://github.com/PacificBiosciences/pbsv" + documentation: "https://github.com/PacificBiosciences/pbsv" + tool_dev_url: "https://github.com/PacificBiosciences/pbsv" licence: ["BSD-3-clause-Clear"] identifier: "" input: From de912b137f22926cf2666efde2dd85ef8d1f80bd Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Tue, 22 Oct 2024 00:40:45 -0700 Subject: [PATCH 07/31] update --- modules/nf-core/hiphase/environment.yml | 9 --- modules/nf-core/hiphase/main.nf | 91 ---------------------- modules/nf-core/hiphase/meta.yml | 57 -------------- modules/nf-core/hiphase/tests/main.nf.test | 73 ----------------- modules/nf-core/hiphase/tests/tags.yml | 2 - modules/nf-core/humid/tests/main.nf.test | 4 +- modules/nf-core/pbmm2/environment.yml | 9 --- modules/nf-core/pbmm2/main.nf | 86 -------------------- modules/nf-core/pbmm2/meta.yml | 57 -------------- modules/nf-core/pbmm2/tests/main.nf.test | 73 ----------------- modules/nf-core/pbmm2/tests/tags.yml | 2 - 11 files changed, 1 insertion(+), 462 deletions(-) delete mode 100644 modules/nf-core/hiphase/environment.yml delete mode 100644 modules/nf-core/hiphase/main.nf delete mode 100644 modules/nf-core/hiphase/meta.yml delete mode 100644 modules/nf-core/hiphase/tests/main.nf.test delete mode 100644 modules/nf-core/hiphase/tests/tags.yml delete mode 100644 modules/nf-core/pbmm2/environment.yml delete mode 100644 modules/nf-core/pbmm2/main.nf delete mode 100644 modules/nf-core/pbmm2/meta.yml delete mode 100644 modules/nf-core/pbmm2/tests/main.nf.test delete mode 100644 modules/nf-core/pbmm2/tests/tags.yml diff --git a/modules/nf-core/hiphase/environment.yml b/modules/nf-core/hiphase/environment.yml deleted file mode 100644 index cc1b89cdd7c..00000000000 --- a/modules/nf-core/hiphase/environment.yml +++ /dev/null @@ -1,9 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "hiphase" -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - "bioconda::hiphase=1.4.5" diff --git a/modules/nf-core/hiphase/main.nf b/modules/nf-core/hiphase/main.nf deleted file mode 100644 index a1ddf21eb58..00000000000 --- a/modules/nf-core/hiphase/main.nf +++ /dev/null @@ -1,91 +0,0 @@ -// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :) -// https://github.com/nf-core/modules/tree/master/modules/nf-core/ -// You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace: -// https://nf-co.re/join -// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters. -// All other parameters MUST be provided using the "task.ext" directive, see here: -// https://www.nextflow.io/docs/latest/process.html#ext -// where "task.ext" is a string. -// Any parameters that need to be evaluated in the context of a particular sample -// e.g. single-end/paired-end data MUST also be defined and evaluated appropriately. -// TODO nf-core: Software that can be piped together SHOULD be added to separate module files -// unless there is a run-time, storage advantage in implementing in this way -// e.g. it's ok to have a single module for bwa to output BAM instead of SAM: -// bwa mem | samtools view -B -T ref.fasta -// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty -// list (`[]`) instead of a file can be used to work around this issue. - -process HIPHASE { - tag "$meta.id" - label 'process_single' - - // TODO nf-core: List required Conda package(s). - // Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10"). - // For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems. - // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below. - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/hiphase:1.4.5--h9ee0642_0': - 'biocontainers/hiphase:1.4.5--h9ee0642_0' }" - - input: - // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group" - // MUST be provided as an input via a Groovy Map called "meta". - // This information may not be required in some instances e.g. indexing reference genome files: - // https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf - // TODO nf-core: Where applicable please provide/convert compressed files as input/output - // e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc. - tuple val(meta), path(bam) - - output: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.bam"), emit: bam - // TODO nf-core: List additional required output channels/values here - 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}" - // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10 - // If the software is unable to output a version number on the command-line then it can be manually specified - // e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf - // Each software used MUST provide the software name and version number in the YAML version file (versions.yml) - // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive - // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter - // using the Nextflow "task" variable e.g. "--threads $task.cpus" - // TODO nf-core: Please replace the example samtools command below with your module's command - // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;) - """ - samtools \\ - sort \\ - $args \\ - -@ $task.cpus \\ - -o ${prefix}.bam \\ - -T $prefix \\ - $bam - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hiphase: \$(samtools --version |& sed '1!d ; s/samtools //') - END_VERSIONS - """ - - stub: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - // TODO nf-core: A stub section should mimic the execution of the original module as best as possible - // Have a look at the following examples: - // Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63 - // Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54 - """ - touch ${prefix}.bam - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hiphase: \$(samtools --version |& sed '1!d ; s/samtools //') - END_VERSIONS - """ -} diff --git a/modules/nf-core/hiphase/meta.yml b/modules/nf-core/hiphase/meta.yml deleted file mode 100644 index f0df5dfec51..00000000000 --- a/modules/nf-core/hiphase/meta.yml +++ /dev/null @@ -1,57 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json -name: "hiphase" -## TODO nf-core: Add a description of the module and list keywords -description: write your description here -keywords: - - sort - - example - - genomics -tools: - - "hiphase": - ## TODO nf-core: Add a description and other details for the software below - description: "Small and structural variant phasing tool for PacBio HiFi reads" - homepage: "None" - documentation: "None" - tool_dev_url: "None" - doi: "" - licence: ['BSD-3-clause-Clear'] - -## TODO nf-core: Add a description of all of the variables used as input -input: - # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - ## TODO nf-core: Delete / customise this example input - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - -## TODO nf-core: Add a description of all of the variables used as output -output: - #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - ## TODO nf-core: Delete / customise this example output - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - -authors: - - "@tanyasarkjain" -maintainers: - - "@tanyasarkjain" diff --git a/modules/nf-core/hiphase/tests/main.nf.test b/modules/nf-core/hiphase/tests/main.nf.test deleted file mode 100644 index f5fa06cda68..00000000000 --- a/modules/nf-core/hiphase/tests/main.nf.test +++ /dev/null @@ -1,73 +0,0 @@ -// TODO nf-core: Once you have added the required tests, please run the following command to build this file: -// nf-core modules test hiphase -nextflow_process { - - name "Test Process HIPHASE" - script "../main.nf" - process "HIPHASE" - - tag "modules" - tag "modules_nfcore" - tag "hiphase" - - // TODO nf-core: Change the test name preferably indicating the test-data and file-format used - test("sarscov2 - bam") { - - // TODO nf-core: If you are created a test for a chained module - // (the module requires running more than one process to generate the required output) - // add the 'setup' method here. - // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules). - - when { - process { - """ - // TODO nf-core: define inputs of the process here. Example: - - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - //TODO nf-core: Add all required assertions to verify the test output. - // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples. - ) - } - - } - - // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix. - test("sarscov2 - bam - stub") { - - options "-stub" - - when { - process { - """ - // TODO nf-core: define inputs of the process here. Example: - - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - //TODO nf-core: Add all required assertions to verify the test output. - ) - } - - } - -} diff --git a/modules/nf-core/hiphase/tests/tags.yml b/modules/nf-core/hiphase/tests/tags.yml deleted file mode 100644 index 33a31bb1dc0..00000000000 --- a/modules/nf-core/hiphase/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -hiphase: - - "modules/nf-core/hiphase/**" diff --git a/modules/nf-core/humid/tests/main.nf.test b/modules/nf-core/humid/tests/main.nf.test index 3d0b839ac1e..987bc20cc03 100644 --- a/modules/nf-core/humid/tests/main.nf.test +++ b/modules/nf-core/humid/tests/main.nf.test @@ -77,9 +77,7 @@ nextflow_process { { assert snapshot(process.out.log, process.out.stats, process.out.versions).match()}, - { - println process.out.dedup[0][1] - assert file(process.out.dedup[0][1].find { + {assert file(process.out.dedup[0][1].find { file(it).name == "test_1_dedup.fastq.gz" }).exists()}, {assert file(process.out.dedup[0][1].find { file(it).name == "test_2_dedup.fastq.gz" }).exists()}, diff --git a/modules/nf-core/pbmm2/environment.yml b/modules/nf-core/pbmm2/environment.yml deleted file mode 100644 index ccddb46fed5..00000000000 --- a/modules/nf-core/pbmm2/environment.yml +++ /dev/null @@ -1,9 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "pbmm2" -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - "bioconda::pbmm2=1.14.99" diff --git a/modules/nf-core/pbmm2/main.nf b/modules/nf-core/pbmm2/main.nf deleted file mode 100644 index 685262719f0..00000000000 --- a/modules/nf-core/pbmm2/main.nf +++ /dev/null @@ -1,86 +0,0 @@ -// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :) -// https://github.com/nf-core/modules/tree/master/modules/nf-core/ -// You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace: -// https://nf-co.re/join -// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters. -// All other parameters MUST be provided using the "task.ext" directive, see here: -// https://www.nextflow.io/docs/latest/process.html#ext -// where "task.ext" is a string. -// Any parameters that need to be evaluated in the context of a particular sample -// e.g. single-end/paired-end data MUST also be defined and evaluated appropriately. -// TODO nf-core: Software that can be piped together SHOULD be added to separate module files -// unless there is a run-time, storage advantage in implementing in this way -// e.g. it's ok to have a single module for bwa to output BAM instead of SAM: -// bwa mem | samtools view -B -T ref.fasta -// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty -// list (`[]`) instead of a file can be used to work around this issue. - -process PBMM2 { - tag "$meta.id" - label 'process_single' - - // TODO nf-core: List required Conda package(s). - // Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10"). - // For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems. - // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below. - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pbmm2:1.14.99--h9ee0642_0': - 'biocontainers/pbmm2:1.14.99--h9ee0642_0' }" - - input: - // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group" - // MUST be provided as an input via a Groovy Map called "meta". - // This information may not be required in some instances e.g. indexing reference genome files: - // https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf - // TODO nf-core: Where applicable please provide/convert compressed files as input/output - // e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc. - tuple val(meta), path(bam) - tuple val(meta), path(fasta) - - output: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.bam"), emit: bam - // TODO nf-core: List additional required output channels/values here - 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}" - // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10 - // If the software is unable to output a version number on the command-line then it can be manually specified - // e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf - // Each software used MUST provide the software name and version number in the YAML version file (versions.yml) - // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive - // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter - // using the Nextflow "task" variable e.g. "--threads $task.cpus" - // TODO nf-core: Please replace the example samtools command below with your module's command - // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;) - """ - pbmm2 align $fasta \${bam} \${bam} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - pbmm2: \$(samtools --version |& sed '1!d ; s/samtools //') - END_VERSIONS - """ - - stub: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - // TODO nf-core: A stub section should mimic the execution of the original module as best as possible - // Have a look at the following examples: - // Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63 - // Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54 - """ - touch ${prefix}.bam - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - pbmm2: \$(samtools --version |& sed '1!d ; s/samtools //') - END_VERSIONS - """ -} diff --git a/modules/nf-core/pbmm2/meta.yml b/modules/nf-core/pbmm2/meta.yml deleted file mode 100644 index 891060201f9..00000000000 --- a/modules/nf-core/pbmm2/meta.yml +++ /dev/null @@ -1,57 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json -name: "pbmm2" -## TODO nf-core: Add a description of the module and list keywords -description: write your description here -keywords: - - sort - - example - - genomics -tools: - - "pbmm2": - ## TODO nf-core: Add a description and other details for the software below - description: "A minimap2 frontend for PacBio native data formats" - homepage: "None" - documentation: "None" - tool_dev_url: "None" - doi: "" - licence: ['BSD-3-clause-Clear'] - -## TODO nf-core: Add a description of all of the variables used as input -input: - # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - ## TODO nf-core: Delete / customise this example input - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - -## TODO nf-core: Add a description of all of the variables used as output -output: - #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - ## TODO nf-core: Delete / customise this example output - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - -authors: - - "@tanyasarkjain" -maintainers: - - "@tanyasarkjain" diff --git a/modules/nf-core/pbmm2/tests/main.nf.test b/modules/nf-core/pbmm2/tests/main.nf.test deleted file mode 100644 index 2c382a75601..00000000000 --- a/modules/nf-core/pbmm2/tests/main.nf.test +++ /dev/null @@ -1,73 +0,0 @@ -// TODO nf-core: Once you have added the required tests, please run the following command to build this file: -// nf-core modules test pbmm2 -nextflow_process { - - name "Test Process PBMM2" - script "../main.nf" - process "PBMM2" - - tag "modules" - tag "modules_nfcore" - tag "pbmm2" - - // TODO nf-core: Change the test name preferably indicating the test-data and file-format used - test("pbmm2 - bam") { - - // TODO nf-core: If you are created a test for a chained module - // (the module requires running more than one process to generate the required output) - // add the 'setup' method here. - // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules). - - when { - process { - """ - // TODO nf-core: define inputs of the process here. Example: - - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - //TODO nf-core: Add all required assertions to verify the test output. - // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples. - ) - } - - } - - // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix. - test("sarscov2 - bam - stub") { - - options "-stub" - - when { - process { - """ - // TODO nf-core: define inputs of the process here. Example: - - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - //TODO nf-core: Add all required assertions to verify the test output. - ) - } - - } - -} diff --git a/modules/nf-core/pbmm2/tests/tags.yml b/modules/nf-core/pbmm2/tests/tags.yml deleted file mode 100644 index 2472daa0786..00000000000 --- a/modules/nf-core/pbmm2/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -pbmm2: - - "modules/nf-core/pbmm2/**" From 763cc708e8b5fb669284dd7fbbe3093c99381b33 Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Tue, 22 Oct 2024 00:42:14 -0700 Subject: [PATCH 08/31] deleting accidental file --- modules/modules | 208 ------------------------------------------------ 1 file changed, 208 deletions(-) delete mode 100644 modules/modules diff --git a/modules/modules b/modules/modules deleted file mode 100644 index e8b417360df..00000000000 --- a/modules/modules +++ /dev/null @@ -1,208 +0,0 @@ ->chr19:45760000-45770300 -catgttggccaggctggtctccaactcctgacctcgagtgatccgcccac -cttggcctcctagagtgctgggattacaggtgtgagccaccgtgcccagc -Ttcccacatcattttacaactactctacgaagcagggtctcctgtggccc -cattttacagataaggaaattgaaatcaaaagactaagctgggcgcggtg -gctcacacctgtaatctcagcagtttgagaggctgacgtaggcggatcac -ctgagatcaggagttcaagaccagcctggccaacatggggaaaccccatt -tctactaaaaatacaagaaGTGTccgggcgtggtggctcacgcctgtaat -cccactattttgggaggccgaggagggcagatcacctgaggtcaggagtt -ggagaccaaccagtctggccatcatggcgaaatactatctctactaaaaa -tacaaaattagccgggtgtggtggtacgtgcctgtaatcccagctactca -ggaggctgaggcagaagaatcgcttaaacctgggaggcgggggttgcagt -aagccaagatggcaccgttggactgcagcctgggcaacaagagcgaaacc -cagtctcaaaaaaggaaaagaaaaagaaaaagaaaTTATCAGGGTGTggc -cgggcgtggtggctcatgcctatacttctagcactttgggaggctgaggc -gggcagatcacctgaggtcaggagtttaaacctagcttgaccaatatgat -gaaaccccctctctactaaaaatacaaaattagctgggcgtggtggtggg 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-GGGCGAGTGGCCTGGAGAGAGGGAGCAGCAGCCGCCAGCCCAGTTCCCGG -TGCCCTCCCCGCGGGGCGTCAGAGAAGGGAGAGGCCGGCGCTCAGGGTGG -GAGGAGAAGGGTTTGGGTTACAGGGAAACCGGAGCTGGGAAAGGTTCACG -TTTCACAACAAAGGCAGAAGACGGACCACGCCGTCCGGGCCCGGAGGGAG -TGTGGGGGCGGGTGGGTAAGAGTAACGGTCAGTGAAGAAAGGGGGCTGGG -AGGCAGCCCCTACGCGGAGTGGAGTGGCCACAGGCCCTGTCCTTTTTCCT -CAGTCCCTCTAGTGCCCCCCGCAGTGTGATTCCCCAACACCGATGGGATT -TGGGAAGGAGCTCGGAATGGAGCCGCTGGAAGAGGAGACGCGTGCGGGGA -GAGGGCCCGGGCGGGTGCCTGTCCCGTCCACACTTAGTCCCCGCGCCCCG -CGGGCGCCTGAGATTGTGAGCTGGTCCCGGGAGATGTCCGAGGACCTCGG -CGCGCCGGCCCCAGCAGTGGGCACGGGGGAAGAGGGCTGGTGGACGGGAT -GTCCCCGGGAGAGCTGGACTTGCGCCGCCCGAGGCCCCTCACCTCTTGCA -GGGCGCGCCGCCTCCGGCCCCGGTCCGGTCGCGCTGTCGCCGGTTCTTGA -ACCAGTTGCTGACCTGCGTGAGCGACAGGCCGGTGAGTGTGGCCAGGCGG -CGCTTCTCGTCCGGCGTGGGGTAGCGGTTGCCGCGGTAGCAGGCCTTGAG -CGCTGCGCGGGAGCGCTCCTTGAAGCAGTAGACTGTCTCCTCGCCGTCCC -AGATGGTCTTGGGCAGCGGGAACTTCTTGCGCAGTCGATACTTGTCCACT -GCGCCAAGCGCGCGGCCGCGGGCCCGCTCGGCCTCATGGTAGCGCGCGCG -CAGGTAGAGGTCCTGCAGGAAGGCGTGGTGGGCGGCGGGGAAGGGGCGGC -TCTCGAGTAGCCGGTAGAGCTCGGCGTACTCGCCCCGCTGGAAGGCCACC -AGGGCCCGCGCGCGCAACACCGGGTCGCTGCCACGTAGGCGCTCGGCCGG -GGGCAGTGCGCCCAGGAAGCGGCTCAAGCGGCCGGCGTGGCCCGCCTGGA -GCAGCGCCTCGCAGACGCACGCCACCTGCTCGGGCGAGAAGCGGAGGCCC -GTGGGCGGTTCGGAAGCGGCCTCGGGGGGCGACCCGGGGACGCCCGGGGA -TCCCGGGCCCTCAGCTCCCGCAGCCGCTGCGCCCGCCCCGGCCCCGGCCG -CCGCCGCCGCCTCACCCTCGGCCGCCTGCAAAGTCTGCAAGAGCTGGCGC -GCTTCCTCCTCCTCCTCTTCGGTCGCCGCCGCCGCCGCCACCGCCTCCCC -CCCAGCCGCCGGCCCCGCGCTCGGCTCCGCAGGCAAGGTAGCCATGTTTT -GCAACTTTGGGAAGTTcctccctccctctcttcctccctcGGGCTTTCCC -CAGCCTCCTCCCCCACCTGTCCCCCCTTTTCGCCCCCACTCCCCGCTCTT -CTCGATCTTCTTTCTGGCCGACCCTGCGCCCCACGCCGGGAAGGCGAGAT -CCAGCTCTCCACTCGGGTCTCTGTCCCCTTGTGTGTGTCCGTCCCCCTCC -CGTCTGTCTGTGATTCTCCCTTTGTTTTCCCTCCGCCTCTGGCCGCGCTT -TCTGCCTCCCCCCAGCGTGTGCTTCTGGCTCAGGGCCTCAGTTTCCCCAT -CGGGACAACGCAGAAGGTAACGGGCCGTCCAGGAGGACTAAGGGCGCGAA -GCCTCCGCCCCGAGACTGAGCTTCTGCACGCCTCCGTCTCCAGGGTCCTC -TGCAGGCCCCCACATTCCCCATCTCGGCCTGCGCTCCGCCCCTCGGAATT -CCCGGCTCCGCAGGGGGGGCGGGTCTGGCCGGGAGGAGGGGCGGGGAACG -GGCTAGAAAGTTTGCAGCAACTTTTCTCGAGCTTGCGTCCCAGGAGCGGA -TGCGCGTGGCGTGCGCAGGCGCAGTGGAAGGAGGATGGCCGCGCGCGCTG -CCAGCCCAGCCCCCTCTTCTCGACGCTCGGTGGCACAGCTGGGCCACAGC -TGGGCGGGGGCGGTGCCTCCGGGTGGCCCGCTCGCCCTCCTATTGGCCGG -ACGCCAAAGCCCCGCCCCGTGGCTTTTCCTCCCCCAACCCTGATTCGGCC -GCTTCGCATCCCGCTAGCTCCTCCCAGACCTTCGGCCGCCTCCACACGCC -TCCGGATTGGCCCGCTGCGGAGCCTCCGGCCCACAACGCAAACCGCGGAC -ACTGTGGAGTCCAGAGCTTTGGGCAGATGGAGGGCCTTTTATTCGCGAGG -GTCGGGGGTGGGGGTCCTAGGTGGGGACAGACAATAAATACCGAGGAATG -TCGGGGTCTCAGTGCATCCAAAACGTGGATTGGGGTTGTTGGGGGTCCTG -TAGCCTGTCAGCGAGTCGGAGGACGAGGTCAATAAATATCCAAACCGCCG -AAGCGGGCGGAGCCGGCTGGGGCTCCGAGAGCAGCGCAAGTGAGGAGGGG -GGCGCGGGATCCCCGAAAAAGCGGGTTTGGCAAAAGCAAATTTCCCGAGT -AAGCAGGCAGAGATCGCGCCAGACGCTCCCCAGAGCAGGGCGTCATGCAC -AAGAAAGCTTTGCACTTTGCGAACCAACGATAGGTGGGGGTGCGTGGAGG -ATGGAACACGGACGGCCCGGCTTGCTGCCTTCCCAGGCCTGCAGTTTGCC -CATCCACGTCAGGGCCTCAGCCTGGCCGAAAGAAAGAAATGGTCTGTGAT -CCCCCcagcagcagcagcagcagcagcagcagcagcagcagcagcagcag -cagcagcagcagcagcaTTCCCGGCTACAAGGACCCTTCGAgccccgttc -g From a4e0099756360c60e9d212a442eb7a9e4a22e8dd Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Tue, 22 Oct 2024 00:43:06 -0700 Subject: [PATCH 09/31] small tweak --- modules/nf-core/pbsv/e1.fasta | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 modules/nf-core/pbsv/e1.fasta diff --git a/modules/nf-core/pbsv/e1.fasta b/modules/nf-core/pbsv/e1.fasta deleted file mode 100644 index e69de29bb2d..00000000000 From 1ded93773a170c63fe2eca33fc987633a3d7eec3 Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Tue, 22 Oct 2024 00:44:21 -0700 Subject: [PATCH 10/31] updating the meta description --- modules/nf-core/pbsv/meta.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/modules/nf-core/pbsv/meta.yml b/modules/nf-core/pbsv/meta.yml index f17cae43c98..b9f52774b48 100644 --- a/modules/nf-core/pbsv/meta.yml +++ b/modules/nf-core/pbsv/meta.yml @@ -41,9 +41,7 @@ output: pattern: "*.vcf.gz" - "*.vcf": type: file - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` + description: VCF file pattern: "*.vcf.gz" - versions: - versions.yml: From b7a62e528114d3983bc33b06a8b34d24a925cd3f Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Tue, 22 Oct 2024 00:45:08 -0700 Subject: [PATCH 11/31] pretty --- modules/nf-core/pbsv/environment.yml | 2 +- modules/nf-core/pbsv/meta.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/pbsv/environment.yml b/modules/nf-core/pbsv/environment.yml index 0bd59695b49..a48d2440108 100644 --- a/modules/nf-core/pbsv/environment.yml +++ b/modules/nf-core/pbsv/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::pbsv=2.9.0" \ No newline at end of file + - "bioconda::pbsv=2.9.0" diff --git a/modules/nf-core/pbsv/meta.yml b/modules/nf-core/pbsv/meta.yml index b9f52774b48..0979d078f70 100644 --- a/modules/nf-core/pbsv/meta.yml +++ b/modules/nf-core/pbsv/meta.yml @@ -41,7 +41,7 @@ output: pattern: "*.vcf.gz" - "*.vcf": type: file - description: VCF file + description: VCF file pattern: "*.vcf.gz" - versions: - versions.yml: From 23b2631b4b80d8281778dcbad56430064648cd9b Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Tue, 22 Oct 2024 00:57:24 -0700 Subject: [PATCH 12/31] removing trailing space --- modules/nf-core/pbsv/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/pbsv/main.nf b/modules/nf-core/pbsv/main.nf index 0a103ccbf97..beabb4cbed6 100644 --- a/modules/nf-core/pbsv/main.nf +++ b/modules/nf-core/pbsv/main.nf @@ -39,7 +39,7 @@ process PBSV { touch ${prefix}.pbsv.vcf cat <<-END_VERSIONS > versions.yml - "${task.process}": + "${task.process}": pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //') END_VERSIONS """ From e8f1cc8bc1e446e89bad72cc7543363955dc185c Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Tue, 22 Oct 2024 01:09:11 -0700 Subject: [PATCH 13/31] space --- modules/nf-core/pbsv/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/pbsv/main.nf b/modules/nf-core/pbsv/main.nf index beabb4cbed6..2e4a416fcd6 100644 --- a/modules/nf-core/pbsv/main.nf +++ b/modules/nf-core/pbsv/main.nf @@ -43,4 +43,4 @@ process PBSV { pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //') END_VERSIONS """ -} +} \ No newline at end of file From 108d99cedfc98f0944089e4e8f5aa8749d29c4e4 Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Tue, 22 Oct 2024 01:18:56 -0700 Subject: [PATCH 14/31] newline --- modules/nf-core/pbsv/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/pbsv/main.nf b/modules/nf-core/pbsv/main.nf index 2e4a416fcd6..beabb4cbed6 100644 --- a/modules/nf-core/pbsv/main.nf +++ b/modules/nf-core/pbsv/main.nf @@ -43,4 +43,4 @@ process PBSV { pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //') END_VERSIONS """ -} \ No newline at end of file +} From 9c921cf79f7729995fc1b41afb146973e40dcd0d Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Tue, 22 Oct 2024 11:37:46 -0700 Subject: [PATCH 15/31] should pass version test --- modules/nf-core/pbsv/main.nf | 1 - modules/nf-core/pbsv/tests/main.nf.test | 10 +++++----- modules/nf-core/pbsv/tests/main.nf.test.snap | 6 +++--- 3 files changed, 8 insertions(+), 9 deletions(-) diff --git a/modules/nf-core/pbsv/main.nf b/modules/nf-core/pbsv/main.nf index beabb4cbed6..de7533c3c70 100644 --- a/modules/nf-core/pbsv/main.nf +++ b/modules/nf-core/pbsv/main.nf @@ -35,7 +35,6 @@ process PBSV { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.bam touch ${prefix}.pbsv.vcf cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/pbsv/tests/main.nf.test b/modules/nf-core/pbsv/tests/main.nf.test index 5f421f110cf..2acc4ddcb93 100644 --- a/modules/nf-core/pbsv/tests/main.nf.test +++ b/modules/nf-core/pbsv/tests/main.nf.test @@ -11,7 +11,7 @@ nextflow_process { test("pbsv_bam") { when { process { - """ + """ input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true) @@ -29,7 +29,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot(process.out.versions).match("versions") }, - { assert process.out.vcf != null }, + { assert process.out.vcf != null }, { assert file(process.out.vcf[0][1]).name == "test.pbsv.vcf" } ) } @@ -43,15 +43,15 @@ nextflow_process { when { process { - """ + """ input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true) - ] + ] input[1] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true) - ] + ] """ } } diff --git a/modules/nf-core/pbsv/tests/main.nf.test.snap b/modules/nf-core/pbsv/tests/main.nf.test.snap index 4d73565e94e..5fecb200a5a 100644 --- a/modules/nf-core/pbsv/tests/main.nf.test.snap +++ b/modules/nf-core/pbsv/tests/main.nf.test.snap @@ -24,7 +24,7 @@ ] ], "1": [ - "versions.yml:md5,78a8c3eb6a67916a463a6d1dfaa4fae4" + "versions.yml:md5,114b69a5e731b0691d6e523c12f7a8ca" ], "vcf": [ [ @@ -36,7 +36,7 @@ ] ], "versions": [ - "versions.yml:md5,78a8c3eb6a67916a463a6d1dfaa4fae4" + "versions.yml:md5,114b69a5e731b0691d6e523c12f7a8ca" ] } ], @@ -44,6 +44,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T17:34:55.61846" + "timestamp": "2024-10-22T11:36:42.780849" } } \ No newline at end of file From d79b6f1b76a9a45a17271d6f25815c452c56ee25 Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Mon, 28 Oct 2024 11:30:43 -0700 Subject: [PATCH 16/31] changed pbsv to pbsv/discover - seperating functionality --- .../pbsv/{ => discover}/environment.yml | 0 modules/nf-core/pbsv/{ => discover}/main.nf | 13 ++-- modules/nf-core/pbsv/{ => discover}/meta.yml | 32 ++++----- .../pbsv/{ => discover}/tests/main.nf.test | 14 ++-- .../pbsv/discover/tests/main.nf.test.snap | 67 +++++++++++++++++++ modules/nf-core/pbsv/tests/main.nf.test.snap | 49 -------------- modules/nf-core/pbsv/tests/tags.yml | 2 - 7 files changed, 95 insertions(+), 82 deletions(-) rename modules/nf-core/pbsv/{ => discover}/environment.yml (100%) rename modules/nf-core/pbsv/{ => discover}/main.nf (82%) rename modules/nf-core/pbsv/{ => discover}/meta.yml (68%) rename modules/nf-core/pbsv/{ => discover}/tests/main.nf.test (83%) create mode 100644 modules/nf-core/pbsv/discover/tests/main.nf.test.snap delete mode 100644 modules/nf-core/pbsv/tests/main.nf.test.snap delete mode 100644 modules/nf-core/pbsv/tests/tags.yml diff --git a/modules/nf-core/pbsv/environment.yml b/modules/nf-core/pbsv/discover/environment.yml similarity index 100% rename from modules/nf-core/pbsv/environment.yml rename to modules/nf-core/pbsv/discover/environment.yml diff --git a/modules/nf-core/pbsv/main.nf b/modules/nf-core/pbsv/discover/main.nf similarity index 82% rename from modules/nf-core/pbsv/main.nf rename to modules/nf-core/pbsv/discover/main.nf index de7533c3c70..0753870c2e4 100644 --- a/modules/nf-core/pbsv/main.nf +++ b/modules/nf-core/pbsv/discover/main.nf @@ -1,7 +1,6 @@ -process PBSV { +process PBSV_DISCOVER { tag "$meta.id" label 'process_single' - conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pbsv:2.9.0--h9ee0642_0': @@ -12,7 +11,7 @@ process PBSV { tuple val(meta2), path(fasta) output: - tuple val(meta), path("*.vcf"), emit: vcf + tuple val(meta), path("*.svsig.gz"), emit: svsig path "versions.yml" , emit: versions when: @@ -22,9 +21,7 @@ process PBSV { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - pbsv discover ${bam} ${prefix}.svsig.gz - pbsv call -j ${task.cpus} ${fasta} ${prefix}.svsig.gz ${prefix}.pbsv.vcf - + pbsv discover ${bam} ${prefix}.pbsv.svsig.gz cat <<-END_VERSIONS > versions.yml "${task.process}": pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //') @@ -35,7 +32,9 @@ process PBSV { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.pbsv.vcf + echo "test" > test.txt + gzip test.txt + mv test.txt.gz ${prefix}.pbsv.svsig.gz cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/pbsv/meta.yml b/modules/nf-core/pbsv/discover/meta.yml similarity index 68% rename from modules/nf-core/pbsv/meta.yml rename to modules/nf-core/pbsv/discover/meta.yml index 0979d078f70..60a43613b48 100644 --- a/modules/nf-core/pbsv/meta.yml +++ b/modules/nf-core/pbsv/discover/meta.yml @@ -1,10 +1,10 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json -name: "pbsv" -description: Pacbio Structural Variant Caller in reads +name: "pbsv_discover" +description: "pbsv - PacBio structural variant (SV) signature discovery tool" keywords: - - structural variants - - long-read analysis - - sequence analysis + - sort + - example + - genomics tools: - "pbsv": description: "pbsv - PacBio structural variant (SV) calling and analysis tools" @@ -21,28 +21,28 @@ input: e.g. `[ id:'sample1', single_end:false ]` - bam: type: file - description: "A BAM file containing an aligned reads" - pattern: "*.bam" + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" - - meta2: type: map description: | - Groovy Map containing reference information - e.g. [ id:'test' ] + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` - fasta: type: file - description: Fasta file + description: fasta file + pattern: "*.fasta" output: - - vcf: + - svsig: - meta: - type: map + type: file description: | Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]` - pattern: "*.vcf.gz" - - "*.vcf": + - "*.svsig.gz": type: file - description: VCF file - pattern: "*.vcf.gz" + description: structural variant signatures files + pattern: "*.svsig.gz" - versions: - versions.yml: type: file diff --git a/modules/nf-core/pbsv/tests/main.nf.test b/modules/nf-core/pbsv/discover/tests/main.nf.test similarity index 83% rename from modules/nf-core/pbsv/tests/main.nf.test rename to modules/nf-core/pbsv/discover/tests/main.nf.test index 2acc4ddcb93..4f564bf267e 100644 --- a/modules/nf-core/pbsv/tests/main.nf.test +++ b/modules/nf-core/pbsv/discover/tests/main.nf.test @@ -1,12 +1,13 @@ nextflow_process { - name "Test Process PBSV" + name "Test Process PBSV_DISCOVER" script "../main.nf" - process "PBSV" + process "PBSV_DISCOVER" tag "modules" tag "modules_nfcore" tag "pbsv" + tag "pbsv/discover" test("pbsv_bam") { when { @@ -29,8 +30,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot(process.out.versions).match("versions") }, - { assert process.out.vcf != null }, - { assert file(process.out.vcf[0][1]).name == "test.pbsv.vcf" } + { assert snapshot(process.out.svsig).match("svsig")} ) } @@ -50,8 +50,8 @@ nextflow_process { ] input[1] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true) - ] + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true) + ] """ } } @@ -62,7 +62,5 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/pbsv/discover/tests/main.nf.test.snap b/modules/nf-core/pbsv/discover/tests/main.nf.test.snap new file mode 100644 index 00000000000..99d160a2158 --- /dev/null +++ b/modules/nf-core/pbsv/discover/tests/main.nf.test.snap @@ -0,0 +1,67 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,0cccc59cd231b14091d7a798e2aacc9a" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-27T22:36:17.825388" + }, + "svsig": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.pbsv.svsig.gz:md5,d2661dc9e6b301267aa7b271a0b70d30" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-28T10:45:01.755567" + }, + "pbsv_bam_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.pbsv.svsig.gz:md5,d8e8fca2dc0f896fd7cb4cb0031ba249" + ] + ], + "1": [ + "versions.yml:md5,0cccc59cd231b14091d7a798e2aacc9a" + ], + "svsig": [ + [ + { + "id": "test", + "single_end": false + }, + "test.pbsv.svsig.gz:md5,d8e8fca2dc0f896fd7cb4cb0031ba249" + ] + ], + "versions": [ + "versions.yml:md5,0cccc59cd231b14091d7a798e2aacc9a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-28T10:41:51.790882" + } +} \ No newline at end of file diff --git a/modules/nf-core/pbsv/tests/main.nf.test.snap b/modules/nf-core/pbsv/tests/main.nf.test.snap deleted file mode 100644 index 5fecb200a5a..00000000000 --- a/modules/nf-core/pbsv/tests/main.nf.test.snap +++ /dev/null @@ -1,49 +0,0 @@ -{ - "versions": { - "content": [ - [ - "versions.yml:md5,114b69a5e731b0691d6e523c12f7a8ca" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-21T17:23:23.323954" - }, - "pbsv_bam_stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.pbsv.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - "versions.yml:md5,114b69a5e731b0691d6e523c12f7a8ca" - ], - "vcf": [ - [ - { - "id": "test", - "single_end": false - }, - "test.pbsv.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,114b69a5e731b0691d6e523c12f7a8ca" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-22T11:36:42.780849" - } -} \ No newline at end of file diff --git a/modules/nf-core/pbsv/tests/tags.yml b/modules/nf-core/pbsv/tests/tags.yml deleted file mode 100644 index 59ab3754578..00000000000 --- a/modules/nf-core/pbsv/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -pbsv: - - "modules/nf-core/pbsv/**" From ba15e72c1faead81b357b5c69496cbb33fc4b144 Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Wed, 30 Oct 2024 20:17:15 -0700 Subject: [PATCH 17/31] pbsv/call --- .../pbsv/{discover => call}/environment.yml | 0 .../nf-core/pbsv/{discover => call}/main.nf | 26 ++++--- .../nf-core/pbsv/{discover => call}/meta.yml | 34 ++++------ modules/nf-core/pbsv/call/tests/main.nf.test | 68 +++++++++++++++++++ .../nf-core/pbsv/call/tests/main.nf.test.snap | 51 ++++++++++++++ modules/nf-core/pbsv/call_2/environment.yml | 7 ++ modules/nf-core/pbsv/call_2/main.nf | 47 +++++++++++++ modules/nf-core/pbsv/call_2/meta.yml | 63 +++++++++++++++++ .../{discover => call_2}/tests/main.nf.test | 22 +++--- .../pbsv/discover/tests/main.nf.test.snap | 67 ------------------ 10 files changed, 278 insertions(+), 107 deletions(-) rename modules/nf-core/pbsv/{discover => call}/environment.yml (100%) rename modules/nf-core/pbsv/{discover => call}/main.nf (66%) rename modules/nf-core/pbsv/{discover => call}/meta.yml (59%) create mode 100644 modules/nf-core/pbsv/call/tests/main.nf.test create mode 100644 modules/nf-core/pbsv/call/tests/main.nf.test.snap create mode 100644 modules/nf-core/pbsv/call_2/environment.yml create mode 100644 modules/nf-core/pbsv/call_2/main.nf create mode 100644 modules/nf-core/pbsv/call_2/meta.yml rename modules/nf-core/pbsv/{discover => call_2}/tests/main.nf.test (73%) delete mode 100644 modules/nf-core/pbsv/discover/tests/main.nf.test.snap diff --git a/modules/nf-core/pbsv/discover/environment.yml b/modules/nf-core/pbsv/call/environment.yml similarity index 100% rename from modules/nf-core/pbsv/discover/environment.yml rename to modules/nf-core/pbsv/call/environment.yml diff --git a/modules/nf-core/pbsv/discover/main.nf b/modules/nf-core/pbsv/call/main.nf similarity index 66% rename from modules/nf-core/pbsv/discover/main.nf rename to modules/nf-core/pbsv/call/main.nf index 0753870c2e4..067e0f76571 100644 --- a/modules/nf-core/pbsv/discover/main.nf +++ b/modules/nf-core/pbsv/call/main.nf @@ -1,17 +1,17 @@ -process PBSV_DISCOVER { +process PBSV_CALL { tag "$meta.id" label 'process_single' - conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pbsv:2.9.0--h9ee0642_0': - 'biocontainers/pbsv:2.9.0--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/pbsv:2.9.0--h9ee0642_0': + 'biocontainers/pbsv:2.9.0--h9ee0642_0' }" input: - tuple val(meta), path(bam) + tuple val(meta), path(svsig) tuple val(meta2), path(fasta) output: - tuple val(meta), path("*.svsig.gz"), emit: svsig + tuple val(meta), path("*.vcf"), emit: vcf path "versions.yml" , emit: versions when: @@ -21,7 +21,13 @@ process PBSV_DISCOVER { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - pbsv discover ${bam} ${prefix}.pbsv.svsig.gz + pbsv call \\ + -j ${task.cpus} \\ + ${fasta} \\ + ${svsig} \\ + ${args} \\ + ${prefix}.vcf \\ + cat <<-END_VERSIONS > versions.yml "${task.process}": pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //') @@ -32,13 +38,11 @@ process PBSV_DISCOVER { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - echo "test" > test.txt - gzip test.txt - mv test.txt.gz ${prefix}.pbsv.svsig.gz + touch ${prefix}.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //') END_VERSIONS """ -} +} \ No newline at end of file diff --git a/modules/nf-core/pbsv/discover/meta.yml b/modules/nf-core/pbsv/call/meta.yml similarity index 59% rename from modules/nf-core/pbsv/discover/meta.yml rename to modules/nf-core/pbsv/call/meta.yml index 60a43613b48..939c3d7dd58 100644 --- a/modules/nf-core/pbsv/discover/meta.yml +++ b/modules/nf-core/pbsv/call/meta.yml @@ -1,48 +1,44 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json -name: "pbsv_discover" -description: "pbsv - PacBio structural variant (SV) signature discovery tool" +name: "pbsv_call" +description: "pbsv/call - PacBio structural variant (SV) calling and analysis tools" keywords: - - sort - - example + - variant + - pacbio - genomics tools: - "pbsv": description: "pbsv - PacBio structural variant (SV) calling and analysis tools" - homepage: "https://github.com/PacificBiosciences/pbsv" - documentation: "https://github.com/PacificBiosciences/pbsv" - tool_dev_url: "https://github.com/PacificBiosciences/pbsv" + homepage: "https://github.com/PacificBiosciences/" + documentation: "https://github.com/PacificBiosciences/" + tool_dev_url: "https://github.com/PacificBiosciences/" licence: ["BSD-3-clause-Clear"] - identifier: "" input: - - meta: type: map description: | Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]` - - bam: + - svsig: type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + description: structural variant file - - meta2: type: map description: | Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` + e.g. `[ id:'reference']` - fasta: type: file - description: fasta file - pattern: "*.fasta" + description: fasta file used as reference output: - - svsig: + - vcf: - meta: - type: file + type: map description: | Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]` - - "*.svsig.gz": + - "*.vcf": type: file - description: structural variant signatures files - pattern: "*.svsig.gz" + description: structural variant file - versions: - versions.yml: type: file diff --git a/modules/nf-core/pbsv/call/tests/main.nf.test b/modules/nf-core/pbsv/call/tests/main.nf.test new file mode 100644 index 00000000000..bc2c48f91c6 --- /dev/null +++ b/modules/nf-core/pbsv/call/tests/main.nf.test @@ -0,0 +1,68 @@ +nextflow_process { + name "Test Process PBSV_CALL" + script "../main.nf" + process "PBSV_CALL" + + tag "modules" + tag "modules_nfcore" + tag "pbsv" + tag "pbsv/call" + + test("pbsv-call - [svsig] [fasta]") { + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/svsig/NA03697B2_new.pbmm2.repeats.svsig.gz', checkIfExists: true) + ] + + input[1] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true) + ] + """ + } + } + + then { + def vcfFile = path(process.out.vcf[0][1]).vcf + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + process.out.versions, + vcfFile.variantsMD5).match() }, + { assert vcfFile.chromosomes == ['chr19:45760000-45770300'] as Set} + ) + } + } + + test("pbsv-call - [svsig] [fasta] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/svsig/NA03697B2_new.pbmm2.repeats.svsig.gz', checkIfExists: true) + ] + + input[1] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/pbsv/call/tests/main.nf.test.snap b/modules/nf-core/pbsv/call/tests/main.nf.test.snap new file mode 100644 index 00000000000..f8a21d61217 --- /dev/null +++ b/modules/nf-core/pbsv/call/tests/main.nf.test.snap @@ -0,0 +1,51 @@ +{ + "pbsv-call - [svsig] [fasta]": { + "content": [ + "test.vcf", + [ + "versions.yml:md5,a8d62b1557c995607b315babfe0bd28b" + ], + "39821c95936a6f9539d3ad53e6562f99" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-30T16:50:00.253251" + }, + "pbsv-call - [svsig] [fasta] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,a8d62b1557c995607b315babfe0bd28b" + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,a8d62b1557c995607b315babfe0bd28b" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-30T16:38:08.198998" + } +} \ No newline at end of file diff --git a/modules/nf-core/pbsv/call_2/environment.yml b/modules/nf-core/pbsv/call_2/environment.yml new file mode 100644 index 00000000000..a48d2440108 --- /dev/null +++ b/modules/nf-core/pbsv/call_2/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::pbsv=2.9.0" diff --git a/modules/nf-core/pbsv/call_2/main.nf b/modules/nf-core/pbsv/call_2/main.nf new file mode 100644 index 00000000000..d3a9bf2bda0 --- /dev/null +++ b/modules/nf-core/pbsv/call_2/main.nf @@ -0,0 +1,47 @@ +process PBSV_CALL { + tag "$meta.id" + label 'process_single' + + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pbsv:2.9.0--h9ee0642_0': + 'biocontainers/pbsv:2.9.0--h9ee0642_0' }" + + input: + tuple val(meta), path(svsig) + tuple val(meta2), path(fasta) + + output: + tuple val(meta), path("*.bam"), emit: bam + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + pbsv call \\ + -j ${task.cpus} \\ + ${fasta} \\ + ${svsig} \\ + ${prefix}.vcf \\ + ${args} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + """ + touch ${prefix}.vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/pbsv/call_2/meta.yml b/modules/nf-core/pbsv/call_2/meta.yml new file mode 100644 index 00000000000..266103f0e94 --- /dev/null +++ b/modules/nf-core/pbsv/call_2/meta.yml @@ -0,0 +1,63 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "pbsv_call" +description: "pbsv/call - PacBio structural variant (SV) calling and analysis tools" +keywords: + - variant + - pacbio + - genomics +tools: + - "pbsv": + description: "pbsv - PacBio structural variant (SV) calling and analysis tools" + homepage: "https://github.com/PacificBiosciences/" + documentation: "https://github.com/PacificBiosciences/" + tool_dev_url: "https://github.com/PacificBiosciences/" + licence: ['BSD-3-clause-Clear'] + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + + ## TODO nf-core: Delete / customise this example input + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + ontologies: + - edam: "http://edamontology.org/format_25722" + - edam: "http://edamontology.org/format_2573" + - edam: "http://edamontology.org/format_3462" + + +## TODO nf-core: Add a description of all of the variables used as output +output: + - bam: + #Only when we have meta + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + ## TODO nf-core: Delete / customise this example output + - "*.bam": + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + ontologies: + - edam: "http://edamontology.org/format_25722" + - edam: "http://edamontology.org/format_2573" + - edam: "http://edamontology.org/format_3462" + + - versions: + - "versions.yml": + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@tanyasarkjain" +maintainers: + - "@tanyasarkjain" diff --git a/modules/nf-core/pbsv/discover/tests/main.nf.test b/modules/nf-core/pbsv/call_2/tests/main.nf.test similarity index 73% rename from modules/nf-core/pbsv/discover/tests/main.nf.test rename to modules/nf-core/pbsv/call_2/tests/main.nf.test index 4f564bf267e..4f98930e83c 100644 --- a/modules/nf-core/pbsv/discover/tests/main.nf.test +++ b/modules/nf-core/pbsv/call_2/tests/main.nf.test @@ -1,13 +1,12 @@ nextflow_process { - name "Test Process PBSV_DISCOVER" + name "Test Process PBSV" script "../main.nf" - process "PBSV_DISCOVER" + process "PBSV" tag "modules" tag "modules_nfcore" tag "pbsv" - tag "pbsv/discover" test("pbsv_bam") { when { @@ -15,7 +14,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/svsig/NA03697B2_new.pbmm2.repeats.svsig.gz', checkIfExists: true) ] input[1] = [ @@ -30,7 +29,8 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot(process.out.versions).match("versions") }, - { assert snapshot(process.out.svsig).match("svsig")} + { assert process.out.vcf != null }, + { assert file(process.out.vcf[0][1]).name == "test.pbsv.vcf" } ) } @@ -46,12 +46,12 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true) - ] + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/svsig/NA03697B2_new.pbmm2.repeats.svsig.gz', checkIfExists: true) + ] input[1] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true) - ] + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true) + ] """ } } @@ -62,5 +62,7 @@ nextflow_process { { assert snapshot(process.out).match() } ) } + } -} + +} \ No newline at end of file diff --git a/modules/nf-core/pbsv/discover/tests/main.nf.test.snap b/modules/nf-core/pbsv/discover/tests/main.nf.test.snap deleted file mode 100644 index 99d160a2158..00000000000 --- a/modules/nf-core/pbsv/discover/tests/main.nf.test.snap +++ /dev/null @@ -1,67 +0,0 @@ -{ - "versions": { - "content": [ - [ - "versions.yml:md5,0cccc59cd231b14091d7a798e2aacc9a" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-27T22:36:17.825388" - }, - "svsig": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.pbsv.svsig.gz:md5,d2661dc9e6b301267aa7b271a0b70d30" - ] - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-28T10:45:01.755567" - }, - "pbsv_bam_stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.pbsv.svsig.gz:md5,d8e8fca2dc0f896fd7cb4cb0031ba249" - ] - ], - "1": [ - "versions.yml:md5,0cccc59cd231b14091d7a798e2aacc9a" - ], - "svsig": [ - [ - { - "id": "test", - "single_end": false - }, - "test.pbsv.svsig.gz:md5,d8e8fca2dc0f896fd7cb4cb0031ba249" - ] - ], - "versions": [ - "versions.yml:md5,0cccc59cd231b14091d7a798e2aacc9a" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-28T10:41:51.790882" - } -} \ No newline at end of file From a6f3b0f2c087c8016ee0458957b9247fc69e3e4e Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Wed, 30 Oct 2024 20:17:46 -0700 Subject: [PATCH 18/31] update --- modules/nf-core/pbsv/call_2/environment.yml | 7 -- modules/nf-core/pbsv/call_2/main.nf | 47 ------------- modules/nf-core/pbsv/call_2/meta.yml | 63 ----------------- .../nf-core/pbsv/call_2/tests/main.nf.test | 68 ------------------- 4 files changed, 185 deletions(-) delete mode 100644 modules/nf-core/pbsv/call_2/environment.yml delete mode 100644 modules/nf-core/pbsv/call_2/main.nf delete mode 100644 modules/nf-core/pbsv/call_2/meta.yml delete mode 100644 modules/nf-core/pbsv/call_2/tests/main.nf.test diff --git a/modules/nf-core/pbsv/call_2/environment.yml b/modules/nf-core/pbsv/call_2/environment.yml deleted file mode 100644 index a48d2440108..00000000000 --- a/modules/nf-core/pbsv/call_2/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -channels: - - conda-forge - - bioconda -dependencies: - - "bioconda::pbsv=2.9.0" diff --git a/modules/nf-core/pbsv/call_2/main.nf b/modules/nf-core/pbsv/call_2/main.nf deleted file mode 100644 index d3a9bf2bda0..00000000000 --- a/modules/nf-core/pbsv/call_2/main.nf +++ /dev/null @@ -1,47 +0,0 @@ -process PBSV_CALL { - tag "$meta.id" - label 'process_single' - - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pbsv:2.9.0--h9ee0642_0': - 'biocontainers/pbsv:2.9.0--h9ee0642_0' }" - - input: - tuple val(meta), path(svsig) - tuple val(meta2), path(fasta) - - output: - tuple val(meta), path("*.bam"), emit: bam - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - """ - pbsv call \\ - -j ${task.cpus} \\ - ${fasta} \\ - ${svsig} \\ - ${prefix}.vcf \\ - ${args} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //') - END_VERSIONS - """ - - stub: - def args = task.ext.args ?: '' - """ - touch ${prefix}.vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //') - END_VERSIONS - """ -} diff --git a/modules/nf-core/pbsv/call_2/meta.yml b/modules/nf-core/pbsv/call_2/meta.yml deleted file mode 100644 index 266103f0e94..00000000000 --- a/modules/nf-core/pbsv/call_2/meta.yml +++ /dev/null @@ -1,63 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json -name: "pbsv_call" -description: "pbsv/call - PacBio structural variant (SV) calling and analysis tools" -keywords: - - variant - - pacbio - - genomics -tools: - - "pbsv": - description: "pbsv - PacBio structural variant (SV) calling and analysis tools" - homepage: "https://github.com/PacificBiosciences/" - documentation: "https://github.com/PacificBiosciences/" - tool_dev_url: "https://github.com/PacificBiosciences/" - licence: ['BSD-3-clause-Clear'] - -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - ## TODO nf-core: Delete / customise this example input - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - ontologies: - - edam: "http://edamontology.org/format_25722" - - edam: "http://edamontology.org/format_2573" - - edam: "http://edamontology.org/format_3462" - - -## TODO nf-core: Add a description of all of the variables used as output -output: - - bam: - #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - ## TODO nf-core: Delete / customise this example output - - "*.bam": - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - ontologies: - - edam: "http://edamontology.org/format_25722" - - edam: "http://edamontology.org/format_2573" - - edam: "http://edamontology.org/format_3462" - - - versions: - - "versions.yml": - type: file - description: File containing software versions - pattern: "versions.yml" - -authors: - - "@tanyasarkjain" -maintainers: - - "@tanyasarkjain" diff --git a/modules/nf-core/pbsv/call_2/tests/main.nf.test b/modules/nf-core/pbsv/call_2/tests/main.nf.test deleted file mode 100644 index 4f98930e83c..00000000000 --- a/modules/nf-core/pbsv/call_2/tests/main.nf.test +++ /dev/null @@ -1,68 +0,0 @@ -nextflow_process { - - name "Test Process PBSV" - script "../main.nf" - process "PBSV" - - tag "modules" - tag "modules_nfcore" - tag "pbsv" - - test("pbsv_bam") { - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/svsig/NA03697B2_new.pbmm2.repeats.svsig.gz', checkIfExists: true) - ] - - input[1] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out.versions).match("versions") }, - { assert process.out.vcf != null }, - { assert file(process.out.vcf[0][1]).name == "test.pbsv.vcf" } - ) - } - - - } - - test("pbsv_bam_stub") { - - options "-stub" - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/svsig/NA03697B2_new.pbmm2.repeats.svsig.gz', checkIfExists: true) - ] - input[1] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - - } - -} \ No newline at end of file From e336cd5e2d69c7c4a81a30079c864c3502ebe299 Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Wed, 30 Oct 2024 20:22:15 -0700 Subject: [PATCH 19/31] fixed spacing --- modules/nf-core/pbsv/call/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/pbsv/call/main.nf b/modules/nf-core/pbsv/call/main.nf index 067e0f76571..9c4747a0d11 100644 --- a/modules/nf-core/pbsv/call/main.nf +++ b/modules/nf-core/pbsv/call/main.nf @@ -3,8 +3,8 @@ process PBSV_CALL { label 'process_single' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pbsv:2.9.0--h9ee0642_0': - 'biocontainers/pbsv:2.9.0--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/pbsv:2.9.0--h9ee0642_0': + 'biocontainers/pbsv:2.9.0--h9ee0642_0' }" input: tuple val(meta), path(svsig) From 392466aacc3efebd8d311f9b7d71e46ccd3b8bb7 Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Wed, 30 Oct 2024 20:23:41 -0700 Subject: [PATCH 20/31] adding end line --- modules/nf-core/pbsv/call/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/pbsv/call/main.nf b/modules/nf-core/pbsv/call/main.nf index 9c4747a0d11..77797d426a5 100644 --- a/modules/nf-core/pbsv/call/main.nf +++ b/modules/nf-core/pbsv/call/main.nf @@ -45,4 +45,4 @@ process PBSV_CALL { pbsv: \$(pbsv --version |& sed '1!d ; s/pbsv //') END_VERSIONS """ -} \ No newline at end of file +} From d5f7523fef4b0e71fba1425bad217d17c22eddc1 Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Wed, 30 Oct 2024 22:08:06 -0700 Subject: [PATCH 21/31] small change --- modules/nf-core/pbsv/call/environment.yml | 2 +- modules/nf-core/pbsv/call/main.nf | 2 +- modules/nf-core/pbsv/call/tests/main.nf.test.snap | 3 ++- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/pbsv/call/environment.yml b/modules/nf-core/pbsv/call/environment.yml index a48d2440108..0bd59695b49 100644 --- a/modules/nf-core/pbsv/call/environment.yml +++ b/modules/nf-core/pbsv/call/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::pbsv=2.9.0" + - "bioconda::pbsv=2.9.0" \ No newline at end of file diff --git a/modules/nf-core/pbsv/call/main.nf b/modules/nf-core/pbsv/call/main.nf index 77797d426a5..11ebafa3ff2 100644 --- a/modules/nf-core/pbsv/call/main.nf +++ b/modules/nf-core/pbsv/call/main.nf @@ -25,8 +25,8 @@ process PBSV_CALL { -j ${task.cpus} \\ ${fasta} \\ ${svsig} \\ - ${args} \\ ${prefix}.vcf \\ + ${args} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/pbsv/call/tests/main.nf.test.snap b/modules/nf-core/pbsv/call/tests/main.nf.test.snap index f8a21d61217..39055cca7c2 100644 --- a/modules/nf-core/pbsv/call/tests/main.nf.test.snap +++ b/modules/nf-core/pbsv/call/tests/main.nf.test.snap @@ -1,6 +1,7 @@ { "pbsv-call - [svsig] [fasta]": { "content": [ + "test.vcf", [ "versions.yml:md5,a8d62b1557c995607b315babfe0bd28b" @@ -46,6 +47,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-30T16:38:08.198998" + "timestamp": "2024-10-30T21:38:47.484071" } } \ No newline at end of file From 45ee91a9ad15ce7318b987f3cdbe9d05235706e4 Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Wed, 30 Oct 2024 22:09:28 -0700 Subject: [PATCH 22/31] space --- modules/nf-core/pbsv/call/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/pbsv/call/environment.yml b/modules/nf-core/pbsv/call/environment.yml index 0bd59695b49..a48d2440108 100644 --- a/modules/nf-core/pbsv/call/environment.yml +++ b/modules/nf-core/pbsv/call/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::pbsv=2.9.0" \ No newline at end of file + - "bioconda::pbsv=2.9.0" From c1a93014eb070289dfb5d7eaf85a718f47b067f7 Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Wed, 30 Oct 2024 22:17:49 -0700 Subject: [PATCH 23/31] please work --- modules/nf-core/pbsv/call/main.nf | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/modules/nf-core/pbsv/call/main.nf b/modules/nf-core/pbsv/call/main.nf index 11ebafa3ff2..e8c54349cc9 100644 --- a/modules/nf-core/pbsv/call/main.nf +++ b/modules/nf-core/pbsv/call/main.nf @@ -25,8 +25,7 @@ process PBSV_CALL { -j ${task.cpus} \\ ${fasta} \\ ${svsig} \\ - ${prefix}.vcf \\ - ${args} + ${prefix}.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": From a9ac5ea0aff567891cdf5dd8c10c4e1918c913dd Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Wed, 30 Oct 2024 22:21:05 -0700 Subject: [PATCH 24/31] spacing --- modules/nf-core/pbsv/call/main.nf | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/modules/nf-core/pbsv/call/main.nf b/modules/nf-core/pbsv/call/main.nf index e8c54349cc9..ff8c5ac3b64 100644 --- a/modules/nf-core/pbsv/call/main.nf +++ b/modules/nf-core/pbsv/call/main.nf @@ -21,11 +21,7 @@ process PBSV_CALL { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - pbsv call \\ - -j ${task.cpus} \\ - ${fasta} \\ - ${svsig} \\ - ${prefix}.vcf + pbsv call -j ${task.cpus} ${fasta} ${svsig} ${prefix}.vcf ${args} cat <<-END_VERSIONS > versions.yml "${task.process}": From 5a3aa68b83c3dc5baafb9c3ae2bc241e938aae78 Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Wed, 30 Oct 2024 22:30:12 -0700 Subject: [PATCH 25/31] slight changes --- modules/nf-core/pbsv/call/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/nf-core/pbsv/call/main.nf b/modules/nf-core/pbsv/call/main.nf index ff8c5ac3b64..d7f1effb64b 100644 --- a/modules/nf-core/pbsv/call/main.nf +++ b/modules/nf-core/pbsv/call/main.nf @@ -2,6 +2,7 @@ process PBSV_CALL { tag "$meta.id" label 'process_single' + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pbsv:2.9.0--h9ee0642_0': 'biocontainers/pbsv:2.9.0--h9ee0642_0' }" @@ -21,7 +22,7 @@ process PBSV_CALL { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - pbsv call -j ${task.cpus} ${fasta} ${svsig} ${prefix}.vcf ${args} + pbsv call -j ${task.cpus} ${fasta} ${svsig} ${prefix}.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": From 79179ea5d4f5e1cc96ab1674332f12a27f89680f Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Wed, 30 Oct 2024 22:35:39 -0700 Subject: [PATCH 26/31] args --- modules/nf-core/pbsv/call/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/pbsv/call/main.nf b/modules/nf-core/pbsv/call/main.nf index d7f1effb64b..8076c3f5de3 100644 --- a/modules/nf-core/pbsv/call/main.nf +++ b/modules/nf-core/pbsv/call/main.nf @@ -22,7 +22,7 @@ process PBSV_CALL { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - pbsv call -j ${task.cpus} ${fasta} ${svsig} ${prefix}.vcf + pbsv call -j ${task.cpus} ${fasta} ${svsig} ${prefix}.vcf $args cat <<-END_VERSIONS > versions.yml "${task.process}": From 9d49f85ccf3e29f64c3ae0c9a207416e6f0d44f4 Mon Sep 17 00:00:00 2001 From: tanyasarkjain <67300971+tanyasarkjain@users.noreply.github.com> Date: Thu, 31 Oct 2024 09:39:15 -0700 Subject: [PATCH 27/31] Update modules/nf-core/pbsv/call/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --- modules/nf-core/pbsv/call/main.nf | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/modules/nf-core/pbsv/call/main.nf b/modules/nf-core/pbsv/call/main.nf index 8076c3f5de3..928557240fe 100644 --- a/modules/nf-core/pbsv/call/main.nf +++ b/modules/nf-core/pbsv/call/main.nf @@ -22,7 +22,13 @@ process PBSV_CALL { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - pbsv call -j ${task.cpus} ${fasta} ${svsig} ${prefix}.vcf $args + pbsv \\ + call \\ + $args \\ + -j ${task.cpus} \\ + ${fasta} \\ + ${svsig} \\ + ${prefix}.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": From e0060de5604169814eab8859df74b453de96afa5 Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Thu, 31 Oct 2024 09:57:27 -0700 Subject: [PATCH 28/31] trailing space --- modules/nf-core/pbsv/call/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/pbsv/call/main.nf b/modules/nf-core/pbsv/call/main.nf index 928557240fe..c0c9e96620f 100644 --- a/modules/nf-core/pbsv/call/main.nf +++ b/modules/nf-core/pbsv/call/main.nf @@ -28,7 +28,7 @@ process PBSV_CALL { -j ${task.cpus} \\ ${fasta} \\ ${svsig} \\ - ${prefix}.vcf + ${prefix}.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": From 5b2c44280ad52c420a6439377371d93cb6eae75e Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Fri, 1 Nov 2024 03:24:25 -0700 Subject: [PATCH 29/31] medium --- modules/nf-core/trgt/genotype/environment.yml | 7 ++ modules/nf-core/trgt/genotype/main.nf | 91 +++++++++++++++++++ modules/nf-core/trgt/genotype/meta.yml | 69 ++++++++++++++ .../nf-core/trgt/genotype/tests/main.nf.test | 74 +++++++++++++++ 4 files changed, 241 insertions(+) create mode 100644 modules/nf-core/trgt/genotype/environment.yml create mode 100644 modules/nf-core/trgt/genotype/main.nf create mode 100644 modules/nf-core/trgt/genotype/meta.yml create mode 100644 modules/nf-core/trgt/genotype/tests/main.nf.test diff --git a/modules/nf-core/trgt/genotype/environment.yml b/modules/nf-core/trgt/genotype/environment.yml new file mode 100644 index 00000000000..721e0df3d5f --- /dev/null +++ b/modules/nf-core/trgt/genotype/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::trgt=1.2.0" diff --git a/modules/nf-core/trgt/genotype/main.nf b/modules/nf-core/trgt/genotype/main.nf new file mode 100644 index 00000000000..8dce1846d0f --- /dev/null +++ b/modules/nf-core/trgt/genotype/main.nf @@ -0,0 +1,91 @@ +// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :) +// https://github.com/nf-core/modules/tree/master/modules/nf-core/ +// You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace: +// https://nf-co.re/join +// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters. +// All other parameters MUST be provided using the "task.ext" directive, see here: +// https://www.nextflow.io/docs/latest/process.html#ext +// where "task.ext" is a string. +// Any parameters that need to be evaluated in the context of a particular sample +// e.g. single-end/paired-end data MUST also be defined and evaluated appropriately. +// TODO nf-core: Software that can be piped together SHOULD be added to separate module files +// unless there is a run-time, storage advantage in implementing in this way +// e.g. it's ok to have a single module for bwa to output BAM instead of SAM: +// bwa mem | samtools view -B -T ref.fasta +// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty +// list (`[]`) instead of a file can be used to work around this issue. + +process TRGT_GENOTYPE { + tag "$meta.id" + label 'process_single' + + // TODO nf-core: List required Conda package(s). + // Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10"). + // For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems. + // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below. + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/trgt:1.2.0--h9ee0642_0': + 'biocontainers/trgt:1.2.0--h9ee0642_0' }" + + input: + // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group" + // MUST be provided as an input via a Groovy Map called "meta". + // This information may not be required in some instances e.g. indexing reference genome files: + // https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf + // TODO nf-core: Where applicable please provide/convert compressed files as input/output + // e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc. + tuple val(meta), path(bam) + + output: + // TODO nf-core: Named file extensions MUST be emitted for ALL output channels + tuple val(meta), path("*.bam"), emit: bam + // TODO nf-core: List additional required output channels/values here + 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}" + // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10 + // If the software is unable to output a version number on the command-line then it can be manually specified + // e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf + // Each software used MUST provide the software name and version number in the YAML version file (versions.yml) + // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive + // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter + // using the Nextflow "task" variable e.g. "--threads $task.cpus" + // TODO nf-core: Please replace the example samtools command below with your module's command + // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;) + """ + samtools \\ + sort \\ + $args \\ + -@ $task.cpus \\ + -o ${prefix}.bam \\ + -T $prefix \\ + $bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + trgt: \$(samtools --version |& sed '1!d ; s/samtools //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + // TODO nf-core: A stub section should mimic the execution of the original module as best as possible + // Have a look at the following examples: + // Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63 + // Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54 + """ + touch ${prefix}.bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + trgt: \$(samtools --version |& sed '1!d ; s/samtools //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/trgt/genotype/meta.yml b/modules/nf-core/trgt/genotype/meta.yml new file mode 100644 index 00000000000..cb89ddb98a6 --- /dev/null +++ b/modules/nf-core/trgt/genotype/meta.yml @@ -0,0 +1,69 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "trgt_genotype" +## TODO nf-core: Add a description of the module and list keywords +description: write your description here +keywords: + - sort + - example + - genomics +tools: + - "trgt": + ## TODO nf-core: Add a description and other details for the software below + description: "Tandem repeat genotyping and visualization from PacBio HiFi data" + homepage: "None" + documentation: "None" + tool_dev_url: "None" + doi: "" + licence: ['Pacific Biosciences Software License (https://github.com/PacificBiosciences/trgt/blob/main/LICENSE.md)'] + identifier: + +## TODO nf-core: Add a description of all of the variables used as input +input: + # Only when we have meta + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + + ## TODO nf-core: Delete / customise this example input + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + ontologies: + - edam: "http://edamontology.org/format_25722" + - edam: "http://edamontology.org/format_2573" + - edam: "http://edamontology.org/format_3462" + + +## TODO nf-core: Add a description of all of the variables used as output +output: + - bam: + #Only when we have meta + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + ## TODO nf-core: Delete / customise this example output + - "*.bam": + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + ontologies: + - edam: "http://edamontology.org/format_25722" + - edam: "http://edamontology.org/format_2573" + - edam: "http://edamontology.org/format_3462" + + - versions: + - "versions.yml": + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@tanyasarkjain" +maintainers: + - "@tanyasarkjain" diff --git a/modules/nf-core/trgt/genotype/tests/main.nf.test b/modules/nf-core/trgt/genotype/tests/main.nf.test new file mode 100644 index 00000000000..8340aaad5d2 --- /dev/null +++ b/modules/nf-core/trgt/genotype/tests/main.nf.test @@ -0,0 +1,74 @@ +// TODO nf-core: Once you have added the required tests, please run the following command to build this file: +// nf-core modules test trgt/genotype +nextflow_process { + + name "Test Process TRGT_GENOTYPE" + script "../main.nf" + process "TRGT_GENOTYPE" + + tag "modules" + tag "modules_nfcore" + tag "trgt" + tag "trgt/genotype" + + // TODO nf-core: Change the test name preferably indicating the test-data and file-format used + test("sarscov2 - bam") { + + // TODO nf-core: If you are created a test for a chained module + // (the module requires running more than one process to generate the required output) + // add the 'setup' method here. + // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules). + + when { + process { + """ + // TODO nf-core: define inputs of the process here. Example: + + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + //TODO nf-core: Add all required assertions to verify the test output. + // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples. + ) + } + + } + + // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix. + test("sarscov2 - bam - stub") { + + options "-stub" + + when { + process { + """ + // TODO nf-core: define inputs of the process here. Example: + + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + //TODO nf-core: Add all required assertions to verify the test output. + ) + } + + } + +} From b67c8b6a183d75593951ace6f70c35a9b1a2ce42 Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Fri, 1 Nov 2024 03:24:57 -0700 Subject: [PATCH 30/31] change --- modules/nf-core/trgt/genotype/environment.yml | 7 -- modules/nf-core/trgt/genotype/main.nf | 91 ------------------- modules/nf-core/trgt/genotype/meta.yml | 69 -------------- .../nf-core/trgt/genotype/tests/main.nf.test | 74 --------------- 4 files changed, 241 deletions(-) delete mode 100644 modules/nf-core/trgt/genotype/environment.yml delete mode 100644 modules/nf-core/trgt/genotype/main.nf delete mode 100644 modules/nf-core/trgt/genotype/meta.yml delete mode 100644 modules/nf-core/trgt/genotype/tests/main.nf.test diff --git a/modules/nf-core/trgt/genotype/environment.yml b/modules/nf-core/trgt/genotype/environment.yml deleted file mode 100644 index 721e0df3d5f..00000000000 --- a/modules/nf-core/trgt/genotype/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -channels: - - conda-forge - - bioconda -dependencies: - - "bioconda::trgt=1.2.0" diff --git a/modules/nf-core/trgt/genotype/main.nf b/modules/nf-core/trgt/genotype/main.nf deleted file mode 100644 index 8dce1846d0f..00000000000 --- a/modules/nf-core/trgt/genotype/main.nf +++ /dev/null @@ -1,91 +0,0 @@ -// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :) -// https://github.com/nf-core/modules/tree/master/modules/nf-core/ -// You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace: -// https://nf-co.re/join -// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters. -// All other parameters MUST be provided using the "task.ext" directive, see here: -// https://www.nextflow.io/docs/latest/process.html#ext -// where "task.ext" is a string. -// Any parameters that need to be evaluated in the context of a particular sample -// e.g. single-end/paired-end data MUST also be defined and evaluated appropriately. -// TODO nf-core: Software that can be piped together SHOULD be added to separate module files -// unless there is a run-time, storage advantage in implementing in this way -// e.g. it's ok to have a single module for bwa to output BAM instead of SAM: -// bwa mem | samtools view -B -T ref.fasta -// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty -// list (`[]`) instead of a file can be used to work around this issue. - -process TRGT_GENOTYPE { - tag "$meta.id" - label 'process_single' - - // TODO nf-core: List required Conda package(s). - // Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10"). - // For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems. - // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below. - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trgt:1.2.0--h9ee0642_0': - 'biocontainers/trgt:1.2.0--h9ee0642_0' }" - - input: - // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group" - // MUST be provided as an input via a Groovy Map called "meta". - // This information may not be required in some instances e.g. indexing reference genome files: - // https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf - // TODO nf-core: Where applicable please provide/convert compressed files as input/output - // e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc. - tuple val(meta), path(bam) - - output: - // TODO nf-core: Named file extensions MUST be emitted for ALL output channels - tuple val(meta), path("*.bam"), emit: bam - // TODO nf-core: List additional required output channels/values here - 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}" - // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10 - // If the software is unable to output a version number on the command-line then it can be manually specified - // e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf - // Each software used MUST provide the software name and version number in the YAML version file (versions.yml) - // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive - // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter - // using the Nextflow "task" variable e.g. "--threads $task.cpus" - // TODO nf-core: Please replace the example samtools command below with your module's command - // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;) - """ - samtools \\ - sort \\ - $args \\ - -@ $task.cpus \\ - -o ${prefix}.bam \\ - -T $prefix \\ - $bam - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - trgt: \$(samtools --version |& sed '1!d ; s/samtools //') - END_VERSIONS - """ - - stub: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - // TODO nf-core: A stub section should mimic the execution of the original module as best as possible - // Have a look at the following examples: - // Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63 - // Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54 - """ - touch ${prefix}.bam - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - trgt: \$(samtools --version |& sed '1!d ; s/samtools //') - END_VERSIONS - """ -} diff --git a/modules/nf-core/trgt/genotype/meta.yml b/modules/nf-core/trgt/genotype/meta.yml deleted file mode 100644 index cb89ddb98a6..00000000000 --- a/modules/nf-core/trgt/genotype/meta.yml +++ /dev/null @@ -1,69 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json -name: "trgt_genotype" -## TODO nf-core: Add a description of the module and list keywords -description: write your description here -keywords: - - sort - - example - - genomics -tools: - - "trgt": - ## TODO nf-core: Add a description and other details for the software below - description: "Tandem repeat genotyping and visualization from PacBio HiFi data" - homepage: "None" - documentation: "None" - tool_dev_url: "None" - doi: "" - licence: ['Pacific Biosciences Software License (https://github.com/PacificBiosciences/trgt/blob/main/LICENSE.md)'] - identifier: - -## TODO nf-core: Add a description of all of the variables used as input -input: - # Only when we have meta - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - ## TODO nf-core: Delete / customise this example input - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - ontologies: - - edam: "http://edamontology.org/format_25722" - - edam: "http://edamontology.org/format_2573" - - edam: "http://edamontology.org/format_3462" - - -## TODO nf-core: Add a description of all of the variables used as output -output: - - bam: - #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - ## TODO nf-core: Delete / customise this example output - - "*.bam": - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - ontologies: - - edam: "http://edamontology.org/format_25722" - - edam: "http://edamontology.org/format_2573" - - edam: "http://edamontology.org/format_3462" - - - versions: - - "versions.yml": - type: file - description: File containing software versions - pattern: "versions.yml" - -authors: - - "@tanyasarkjain" -maintainers: - - "@tanyasarkjain" diff --git a/modules/nf-core/trgt/genotype/tests/main.nf.test b/modules/nf-core/trgt/genotype/tests/main.nf.test deleted file mode 100644 index 8340aaad5d2..00000000000 --- a/modules/nf-core/trgt/genotype/tests/main.nf.test +++ /dev/null @@ -1,74 +0,0 @@ -// TODO nf-core: Once you have added the required tests, please run the following command to build this file: -// nf-core modules test trgt/genotype -nextflow_process { - - name "Test Process TRGT_GENOTYPE" - script "../main.nf" - process "TRGT_GENOTYPE" - - tag "modules" - tag "modules_nfcore" - tag "trgt" - tag "trgt/genotype" - - // TODO nf-core: Change the test name preferably indicating the test-data and file-format used - test("sarscov2 - bam") { - - // TODO nf-core: If you are created a test for a chained module - // (the module requires running more than one process to generate the required output) - // add the 'setup' method here. - // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules). - - when { - process { - """ - // TODO nf-core: define inputs of the process here. Example: - - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - //TODO nf-core: Add all required assertions to verify the test output. - // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples. - ) - } - - } - - // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix. - test("sarscov2 - bam - stub") { - - options "-stub" - - when { - process { - """ - // TODO nf-core: define inputs of the process here. Example: - - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - //TODO nf-core: Add all required assertions to verify the test output. - ) - } - - } - -} From 337f0b8b12a1cd0ad2f0c92767f82c4526721e27 Mon Sep 17 00:00:00 2001 From: Tanya Jain Date: Fri, 1 Nov 2024 03:26:00 -0700 Subject: [PATCH 31/31] medium --- modules/nf-core/pbsv/call/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/pbsv/call/main.nf b/modules/nf-core/pbsv/call/main.nf index c0c9e96620f..50be300fd20 100644 --- a/modules/nf-core/pbsv/call/main.nf +++ b/modules/nf-core/pbsv/call/main.nf @@ -1,6 +1,6 @@ process PBSV_CALL { tag "$meta.id" - label 'process_single' + label 'process_medium' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?