From 55a6a27904f2b0d30e10cf741dc54a7c104da882 Mon Sep 17 00:00:00 2001 From: torossee Date: Wed, 19 Jun 2024 10:52:55 +0200 Subject: [PATCH 01/11] merge_cnv: sort cnvs on genomic positions --- modules/local/exomedepth/merge_cnv/main.nf | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/modules/local/exomedepth/merge_cnv/main.nf b/modules/local/exomedepth/merge_cnv/main.nf index d63b4f2..3504d80 100644 --- a/modules/local/exomedepth/merge_cnv/main.nf +++ b/modules/local/exomedepth/merge_cnv/main.nf @@ -1,4 +1,4 @@ -//MERGE CNV CALL FILES +//MERGE AND SORT (ON GENOMIC POSITION) EXOMEDEPTH CNV CALL FILES process CNV_MERGE { tag "$meta" @@ -19,13 +19,15 @@ process CNV_MERGE { script: def prefix = task.ext.prefix ?: "${meta}_CNVs_ExomeDepth" """ - cp $auto "${prefix}.txt" - tail +2 $chrx >> "${prefix}.txt" + { head -n 1 $auto && \ + { tail -n +2 $auto && tail -n +2 $chrx ; } | \ + sort -k7,7V -k5,5n -k6,6n ; } > "${prefix}.txt" cat <<-END_VERSIONS > versions.yml "${task.process}": + head: \$(head --version | sed '1!d; s/head (GNU coreutils) //') tail: \$(tail --version | sed '1!d; s/tail (GNU coreutils) //') - cp: \$(cp --version | sed '1!d; s/cp (GNU coreutils) //') + sort: \$(sort --version | sed '1!d; s/sort (GNU coreutils) //') END_VERSIONS """ From 35d8c293f28e3a3b7edd59a2e9e4f329a45f5929 Mon Sep 17 00:00:00 2001 From: torossee Date: Wed, 19 Jun 2024 11:02:02 +0200 Subject: [PATCH 02/11] update changelog --- CHANGELOG.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c324ad8..ed70b18 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,10 +3,16 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.0.0 - 2024-06-12 +## v1.0.0 - Dashing Doku - [2024-06-12] Initial release of nf-cmgg/exomecnv, created with the [nf-core](https://nf-co.re/) template v2.13. ### `Added` - First release of the pipeline - CNV calling using [ExomeDepth](https://github.com/vplagnol/ExomeDepth) + +## v1.0.1 - [2024-06-19] + +### `Fixes` + +- Sort file of merged CNV calls to fix an issue with TABIX (needs sorted VCF files) From 205583f8744d291d1511c440201d4ab7aa0659ca Mon Sep 17 00:00:00 2001 From: torossee Date: Wed, 19 Jun 2024 11:12:43 +0200 Subject: [PATCH 03/11] bump version 1.0.1 --- assets/multiqc_config.yml | 2 +- nextflow.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index e373493..0135229 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-cmgg/exomecnv + This report has been generated by the nf-cmgg/exomecnv analysis pipeline. report_section_order: "nf-cmgg-exomecnv-methods-description": diff --git a/nextflow.config b/nextflow.config index 774134f..5d5635f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -249,7 +249,7 @@ manifest { description = """A nextflow pipeline for calling exome CNVs""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.0.0' + version = '1.0.1' doi = '' } From 8ea218f346028a3174e1c643927fae2b9b01f205 Mon Sep 17 00:00:00 2001 From: torossee Date: Fri, 21 Jun 2024 16:35:06 +0200 Subject: [PATCH 04/11] index VEP VCF + do not publish BAM files --- CHANGELOG.md | 8 +++++++- conf/modules.config | 6 ++++++ docs/output.md | 3 ++- subworkflows/local/vcf_annotation/main.nf | 10 ++++++++-- workflows/exomecnv.nf | 5 +++-- 5 files changed, 26 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ed70b18..3e46bad 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,8 +11,14 @@ Initial release of nf-cmgg/exomecnv, created with the [nf-core](https://nf-co.re - First release of the pipeline - CNV calling using [ExomeDepth](https://github.com/vplagnol/ExomeDepth) -## v1.0.1 - [2024-06-19] +## v1.0.1 - Lightning Lukaku [2024-06-19] + +### `Improvements` + +- Index the VEP annotated VCF with TABIX +- Do not copy output of SAMTOOLS_CONVERT module (BAM files) to the `publishDir` ### `Fixes` - Sort file of merged CNV calls to fix an issue with TABIX (needs sorted VCF files) + diff --git a/conf/modules.config b/conf/modules.config index 4e76fce..2e43cd2 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -58,4 +58,10 @@ process { mode: params.publish_dir_mode ] } + + withName: 'SAMTOOLS_CONVERT' { + publishDir = [ + enabled: false + ] + } } diff --git a/docs/output.md b/docs/output.md index 951db8e..bba3551 100644 --- a/docs/output.md +++ b/docs/output.md @@ -24,7 +24,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d ### Cram Prepare -If CRAM/CRAI files were provided in the samplesheet, they will be converted into BAM/BAI first before continuing with the pipeline. +If CRAM/CRAI files were provided in the samplesheet, they will be converted into BAM/BAI first before continuing with the pipeline. If the directive `publishDir` option `enabled` is set to `true` (default: `false`) , the BAM/BAI are in the output folder.
Output files @@ -122,6 +122,7 @@ A TBI index file is generated for each VCF file. While these TBI index files are - `vep/` - `.vep.vcf.gz`: VEP annotated file + - `.vep.vcf.gz.tbi`: index of VEP annotated file
diff --git a/subworkflows/local/vcf_annotation/main.nf b/subworkflows/local/vcf_annotation/main.nf index 76dc2cc..3e9c757 100644 --- a/subworkflows/local/vcf_annotation/main.nf +++ b/subworkflows/local/vcf_annotation/main.nf @@ -5,7 +5,7 @@ */ include { ENSEMBLVEP_VEP as VEP } from '../../../modules/nf-core/ensemblvep/vep/main' - +include { TABIX_TABIX as TABIX } from '../../../modules/nf-core/tabix/tabix/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RUN ENSEMBLE VEP WORKFLOW @@ -34,7 +34,13 @@ workflow VCF_ANNOTATION { ch_vep_extra_files ) + // Index VCF file + + TABIX ( VEP.out.vcf ) + emit: vcfs = VEP.out.vcf - versions = VEP.out.versions + tbi = TABIX.out.tbi + versionsvep = VEP.out.versions + versionstbi = TABIX.out.versions } diff --git a/workflows/exomecnv.nf b/workflows/exomecnv.nf index b37d848..90e915c 100644 --- a/workflows/exomecnv.nf +++ b/workflows/exomecnv.nf @@ -65,7 +65,7 @@ workflow EXOMECNV { if (params.annotate) { ANNOTATION_FROM_CRAM ( ch_exomedepth_vcf, ch_fasta, ch_vep_cache ) - ch_versions = ch_versions.mix(ANNOTATION_FROM_CRAM.out.versions) + ch_versions = ch_versions.mix(ANNOTATION_FROM_CRAM.out.versionsvep) } } @@ -81,7 +81,8 @@ workflow EXOMECNV { ANNOTATION_FROM_VCF ( ch_vcf, ch_fasta, ch_vep_cache ) - ch_versions = ch_versions.mix(ANNOTATION_FROM_VCF.out.versions) + ch_versions = ch_versions.mix(ANNOTATION_FROM_VCF.out.versionsvep) + ch_versions = ch_versions.mix(ANNOTATION_FROM_VCF.out.versionstbi) } // Collate and save software versions From 8a39312283f9edf4cf3a813b07ae729dc3c04c88 Mon Sep 17 00:00:00 2001 From: torossee Date: Mon, 24 Jun 2024 13:35:38 +0200 Subject: [PATCH 05/11] fix vep tabix --- conf/modules.config | 8 +++++++- subworkflows/local/vcf_annotation/main.nf | 6 +++--- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 2e43cd2..d27eded 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -52,12 +52,18 @@ process { ].join(' ').trim()} } - withName: 'TABIX_TABIX' { + withName: 'TABIX' { publishDir = [ path: {"$params.outdir/exomedepth/cnv_call"}, mode: params.publish_dir_mode ] } + withName: 'TABIX_VEP' { + publishDir = [ + path: {"$params.outdir/vep"}, + mode: params.publish_dir_mode + ] + } withName: 'SAMTOOLS_CONVERT' { publishDir = [ diff --git a/subworkflows/local/vcf_annotation/main.nf b/subworkflows/local/vcf_annotation/main.nf index 3e9c757..9b945bd 100644 --- a/subworkflows/local/vcf_annotation/main.nf +++ b/subworkflows/local/vcf_annotation/main.nf @@ -5,7 +5,7 @@ */ include { ENSEMBLVEP_VEP as VEP } from '../../../modules/nf-core/ensemblvep/vep/main' -include { TABIX_TABIX as TABIX } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIX_VEP } from '../../../modules/nf-core/tabix/tabix/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RUN ENSEMBLE VEP WORKFLOW @@ -36,11 +36,11 @@ workflow VCF_ANNOTATION { // Index VCF file - TABIX ( VEP.out.vcf ) + TABIX_VEP ( VEP.out.vcf ) emit: vcfs = VEP.out.vcf - tbi = TABIX.out.tbi + tbi = TABIX_VEP.out.tbi versionsvep = VEP.out.versions versionstbi = TABIX.out.versions } From e7b92bde3c4ff815b7f97e993bc80046954c76a4 Mon Sep 17 00:00:00 2001 From: torossee Date: Mon, 24 Jun 2024 13:41:46 +0200 Subject: [PATCH 06/11] fixes --- conf/modules.config | 6 +++++- docs/output.md | 7 ++++--- subworkflows/local/vcf_annotation/main.nf | 2 +- 3 files changed, 10 insertions(+), 5 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index d27eded..9f8bb84 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -50,6 +50,10 @@ process { '--fields "SYMBOL,Gene"', '--transcript_filter "stable_id match ENST"' ].join(' ').trim()} + publishDir = [ + path: {"$params.outdir/exomedepth/cnv_call_vep"}, + mode: params.publish_dir_mode + ] } withName: 'TABIX' { @@ -60,7 +64,7 @@ process { } withName: 'TABIX_VEP' { publishDir = [ - path: {"$params.outdir/vep"}, + path: {"$params.outdir/exomedepth/cnv_call_vep"}, mode: params.publish_dir_mode ] } diff --git a/docs/output.md b/docs/output.md index bba3551..2093425 100644 --- a/docs/output.md +++ b/docs/output.md @@ -120,9 +120,10 @@ A TBI index file is generated for each VCF file. While these TBI index files are
Output files -- `vep/` - - `.vep.vcf.gz`: VEP annotated file - - `.vep.vcf.gz.tbi`: index of VEP annotated file +- `exomedepth/` + - `cnv_call_vep/` + - `.vep.vcf.gz`: VEP annotated file + - `.vep.vcf.gz.tbi`: index of VEP annotated file
diff --git a/subworkflows/local/vcf_annotation/main.nf b/subworkflows/local/vcf_annotation/main.nf index 9b945bd..f592f85 100644 --- a/subworkflows/local/vcf_annotation/main.nf +++ b/subworkflows/local/vcf_annotation/main.nf @@ -42,5 +42,5 @@ workflow VCF_ANNOTATION { vcfs = VEP.out.vcf tbi = TABIX_VEP.out.tbi versionsvep = VEP.out.versions - versionstbi = TABIX.out.versions + versionstbi = TABIX_VEP.out.versions } From 6cfa1a83f3bebeb1afcf4b654335963bed2e9060 Mon Sep 17 00:00:00 2001 From: torossee Date: Tue, 25 Jun 2024 10:22:58 +0200 Subject: [PATCH 07/11] more resources for samtools_convert + update samtools_convert,multiqc --- modules.json | 7 ++++--- modules/local/exomedepth/cnv_call/main.nf | 2 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 ++-- .../nf-core/multiqc/tests/main.nf.test.snap | 18 +++++++++--------- .../nf-core/samtools/convert/environment.yml | 4 ++-- modules/nf-core/samtools/convert/main.nf | 6 +++--- .../samtools/convert/samtools-convert.diff | 13 +++++++++++++ .../samtools/convert/tests/main.nf.test.snap | 16 ++++++++-------- 9 files changed, 43 insertions(+), 29 deletions(-) create mode 100644 modules/nf-core/samtools/convert/samtools-convert.diff diff --git a/modules.json b/modules.json index 126ef39..25637da 100644 --- a/modules.json +++ b/modules.json @@ -17,13 +17,14 @@ }, "multiqc": { "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", + "git_sha": "8f2062e7b4185590fb9f43c275381a31a6544fc0", "installed_by": ["modules"] }, "samtools/convert": { "branch": "master", - "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", - "installed_by": ["modules"] + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", + "installed_by": ["modules"], + "patch": "modules/nf-core/samtools/convert/samtools-convert.diff" }, "tabix/tabix": { "branch": "master", diff --git a/modules/local/exomedepth/cnv_call/main.nf b/modules/local/exomedepth/cnv_call/main.nf index b87b5ea..1848cab 100644 --- a/modules/local/exomedepth/cnv_call/main.nf +++ b/modules/local/exomedepth/cnv_call/main.nf @@ -1,6 +1,6 @@ process CNV_CALL { tag "$sample $meta2.chr" - label 'process_low' + label 'process_medium' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb6..72e598b 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc=1.22.2 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 47ac352..e59efef 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.22.2--pyhdfd78af_0' : + 'biocontainers/multiqc:1.22.2--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index bfebd80..a170c31 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,ddbc971a8307f9b9b7b973714cde29d0" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:48:55.657331" + "timestamp": "2024-06-10T11:50:10.874341679" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,ddbc971a8307f9b9b7b973714cde29d0" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:49.071937" + "timestamp": "2024-06-10T11:50:49.271943761" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,ddbc971a8307f9b9b7b973714cde29d0" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:25.457567" + "timestamp": "2024-06-10T11:50:34.046706025" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml index cd4ee8c..7a95ca6 100644 --- a/modules/nf-core/samtools/convert/environment.yml +++ b/modules/nf-core/samtools/convert/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index d61fbe2..6564737 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -1,11 +1,11 @@ process SAMTOOLS_CONVERT { tag "$meta.id" - label 'process_low' + label 'process_medium' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/samtools/convert/samtools-convert.diff b/modules/nf-core/samtools/convert/samtools-convert.diff new file mode 100644 index 0000000..ff96585 --- /dev/null +++ b/modules/nf-core/samtools/convert/samtools-convert.diff @@ -0,0 +1,13 @@ +Changes in module 'nf-core/samtools/convert' +--- modules/nf-core/samtools/convert/main.nf ++++ modules/nf-core/samtools/convert/main.nf +@@ -1,6 +1,6 @@ + process SAMTOOLS_CONVERT { + tag "$meta.id" +- label 'process_low' ++ label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + +************************************************************ diff --git a/modules/nf-core/samtools/convert/tests/main.nf.test.snap b/modules/nf-core/samtools/convert/tests/main.nf.test.snap index 3d6f88c..5136290 100644 --- a/modules/nf-core/samtools/convert/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/convert/tests/main.nf.test.snap @@ -22,26 +22,26 @@ "cram_to_bam_versions": { "content": [ [ - "versions.yml:md5,dd0aaf61f39c9ce91c74090f3c7ce1d0" + "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-06T11:14:51.308885706" + "timestamp": "2024-05-28T15:44:34.618037105" }, "bam_to_cram_versions": { "content": [ [ - "versions.yml:md5,dd0aaf61f39c9ce91c74090f3c7ce1d0" + "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-06T11:14:36.643960504" + "timestamp": "2024-05-28T15:44:29.165839679" }, "stub": { "content": [ @@ -71,7 +71,7 @@ ] ], "4": [ - "versions.yml:md5,dd0aaf61f39c9ce91c74090f3c7ce1d0" + "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" ], "bai": [ @@ -98,15 +98,15 @@ ] ], "versions": [ - "versions.yml:md5,dd0aaf61f39c9ce91c74090f3c7ce1d0" + "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-05-03T12:01:40.896170698" + "timestamp": "2024-05-28T15:44:40.258233921" }, "bam_to_cram_index": { "content": [ From bcd864edb5027ac890c4ed2aa5ec96581720c0f7 Mon Sep 17 00:00:00 2001 From: torossee Date: Tue, 25 Jun 2024 17:14:41 +0200 Subject: [PATCH 08/11] optimize resources --- modules.json | 35 ++++++++++++++----- modules/local/exomedepth/cnv_call/main.nf | 2 +- .../ensemblvep/vep/ensemblvep-vep.diff | 13 +++++++ modules/nf-core/ensemblvep/vep/main.nf | 2 +- 4 files changed, 41 insertions(+), 11 deletions(-) create mode 100644 modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff diff --git a/modules.json b/modules.json index 25637da..4c1c4fe 100644 --- a/modules.json +++ b/modules.json @@ -8,28 +8,39 @@ "bedgovcf": { "branch": "master", "git_sha": "71a96063a7e09be7ea48f069d134a56ce86c9ba6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ensemblvep/vep": { "branch": "master", "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ], + "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff" }, "multiqc": { "branch": "master", "git_sha": "8f2062e7b4185590fb9f43c275381a31a6544fc0", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/convert": { "branch": "master", "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/samtools/convert/samtools-convert.diff" }, "tabix/tabix": { "branch": "master", "git_sha": "9502adb23c0b97ed8e616bbbdfa73b4585aec9a1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -38,20 +49,26 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/local/exomedepth/cnv_call/main.nf b/modules/local/exomedepth/cnv_call/main.nf index 1848cab..b87b5ea 100644 --- a/modules/local/exomedepth/cnv_call/main.nf +++ b/modules/local/exomedepth/cnv_call/main.nf @@ -1,6 +1,6 @@ process CNV_CALL { tag "$sample $meta2.chr" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff new file mode 100644 index 0000000..8046dab --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff @@ -0,0 +1,13 @@ +Changes in module 'nf-core/ensemblvep/vep' +--- modules/nf-core/ensemblvep/vep/main.nf ++++ modules/nf-core/ensemblvep/vep/main.nf +@@ -1,6 +1,6 @@ + process ENSEMBLVEP_VEP { + tag "$meta.id" +- label 'process_medium' ++ label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + +************************************************************ diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index e82471a..160b240 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -1,6 +1,6 @@ process ENSEMBLVEP_VEP { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? From b352f63a457922cf282f76ce7da91f03a574aa4f Mon Sep 17 00:00:00 2001 From: torossee Date: Wed, 26 Jun 2024 14:24:50 +0200 Subject: [PATCH 09/11] prettier --- CHANGELOG.md | 1 - modules.json | 34 +++++++++------------------------- 2 files changed, 9 insertions(+), 26 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3e46bad..4079f71 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,4 +21,3 @@ Initial release of nf-cmgg/exomecnv, created with the [nf-core](https://nf-co.re ### `Fixes` - Sort file of merged CNV calls to fix an issue with TABIX (needs sorted VCF files) - diff --git a/modules.json b/modules.json index 4c1c4fe..46cb89c 100644 --- a/modules.json +++ b/modules.json @@ -8,39 +8,29 @@ "bedgovcf": { "branch": "master", "git_sha": "71a96063a7e09be7ea48f069d134a56ce86c9ba6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff" }, "multiqc": { "branch": "master", "git_sha": "8f2062e7b4185590fb9f43c275381a31a6544fc0", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/convert": { "branch": "master", "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/samtools/convert/samtools-convert.diff" }, "tabix/tabix": { "branch": "master", "git_sha": "9502adb23c0b97ed8e616bbbdfa73b4585aec9a1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -49,26 +39,20 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} From f8e85ea2ee206f7d1036c0748b90afcf0bbc92fe Mon Sep 17 00:00:00 2001 From: torossee Date: Wed, 26 Jun 2024 14:31:28 +0200 Subject: [PATCH 10/11] changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4079f71..1009252 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,8 @@ Initial release of nf-cmgg/exomecnv, created with the [nf-core](https://nf-co.re - Index the VEP annotated VCF with TABIX - Do not copy output of SAMTOOLS_CONVERT module (BAM files) to the `publishDir` +- update versions of multiqc and samtools_convert modules +- optimize module resources ### `Fixes` From 8e045d82fabb51f1a0b3a900960909e8a31cc7f9 Mon Sep 17 00:00:00 2001 From: torossee Date: Thu, 27 Jun 2024 16:20:51 +0200 Subject: [PATCH 11/11] merge versions --- subworkflows/local/vcf_annotation/main.nf | 7 ++++--- workflows/exomecnv.nf | 5 ++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/vcf_annotation/main.nf b/subworkflows/local/vcf_annotation/main.nf index f592f85..b59773e 100644 --- a/subworkflows/local/vcf_annotation/main.nf +++ b/subworkflows/local/vcf_annotation/main.nf @@ -23,6 +23,7 @@ workflow VCF_ANNOTATION { main: ch_vep_extra_files = [] + ch_versions = Channel.empty() VEP ( ch_vcfs, @@ -33,14 +34,14 @@ workflow VCF_ANNOTATION { fasta, ch_vep_extra_files ) - + ch_versions = ch_versions.mix(VEP.out.versions) // Index VCF file TABIX_VEP ( VEP.out.vcf ) + ch_versions = ch_versions.mix(TABIX_VEP.out.versions) emit: vcfs = VEP.out.vcf tbi = TABIX_VEP.out.tbi - versionsvep = VEP.out.versions - versionstbi = TABIX_VEP.out.versions + versions = ch_versions } diff --git a/workflows/exomecnv.nf b/workflows/exomecnv.nf index 90e915c..b37d848 100644 --- a/workflows/exomecnv.nf +++ b/workflows/exomecnv.nf @@ -65,7 +65,7 @@ workflow EXOMECNV { if (params.annotate) { ANNOTATION_FROM_CRAM ( ch_exomedepth_vcf, ch_fasta, ch_vep_cache ) - ch_versions = ch_versions.mix(ANNOTATION_FROM_CRAM.out.versionsvep) + ch_versions = ch_versions.mix(ANNOTATION_FROM_CRAM.out.versions) } } @@ -81,8 +81,7 @@ workflow EXOMECNV { ANNOTATION_FROM_VCF ( ch_vcf, ch_fasta, ch_vep_cache ) - ch_versions = ch_versions.mix(ANNOTATION_FROM_VCF.out.versionsvep) - ch_versions = ch_versions.mix(ANNOTATION_FROM_VCF.out.versionstbi) + ch_versions = ch_versions.mix(ANNOTATION_FROM_VCF.out.versions) } // Collate and save software versions