From 1038d3de36263159b4138324a646105941ac271a Mon Sep 17 00:00:00 2001 From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Date: Fri, 21 Jul 2023 12:21:08 +0200 Subject: [PATCH 1/3] update metaphlan module (#3661) --- modules/nf-core/metaphlan/metaphlan/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/metaphlan/metaphlan/main.nf b/modules/nf-core/metaphlan/metaphlan/main.nf index 477f1f28ddd..24533571e18 100644 --- a/modules/nf-core/metaphlan/metaphlan/main.nf +++ b/modules/nf-core/metaphlan/metaphlan/main.nf @@ -28,8 +28,8 @@ process METAPHLAN_METAPHLAN { def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt" """ - BT2_DB=`find -L "${metaphlan_db_latest}" -name "*rev.1.bt2l" -exec dirname {} \\;` - BT2_DB_INDEX=`find -L ${metaphlan_db_latest} -name "*.rev.1.bt2l" | sed 's/\\.rev.1.bt2l\$//' | sed 's/.*\\///'` + BT2_DB=`find -L "${metaphlan_db_latest}" -name "*rev.1.bt2*" -exec dirname {} \\;` + BT2_DB_INDEX=`find -L ${metaphlan_db_latest} -name "*.rev.1.bt2*" | sed 's/\\.rev.1.bt2.*\$//' | sed 's/.*\\///'` metaphlan \\ --nproc $task.cpus \\ From 3b63e1df297ef474b0070aa5fabb30d732173671 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Fri, 21 Jul 2023 11:34:40 +0100 Subject: [PATCH 2/3] CNVKit 0.9.10 update (#3651) * upgrade CNVkit to 0.9.10 * homogenise keywords of all CNVkit modules * Add samtools dependency to bam2seqz module of sequenzautils Without specifying the dependency to a more or less current version of samtools, conda solves the environment for sequenza by using a very old samtools version that can cause problems when processing subsampled files (automated tests) * Update cnvkit to 0.9.10 Changes: - Update cnvkit to 0.9.10 - Update samtools in cnvkit modules to 1.17 Based on #3545 authored by @priesgo. * cnvkit 0.9.10 test update * update checksums of output files in tests for CNVkit batch * Update cnvkit/export VCF test * Additional tags for sequenzautils --------- Co-authored-by: Pablo Riesgo-Ferreiro Co-authored-by: Julian Mohr <81371922+JulianMohr@users.noreply.github.com> --- modules/nf-core/cnvkit/access/main.nf | 6 +++--- modules/nf-core/cnvkit/access/meta.yml | 1 + modules/nf-core/cnvkit/antitarget/main.nf | 6 +++--- modules/nf-core/cnvkit/antitarget/meta.yml | 2 ++ modules/nf-core/cnvkit/batch/main.nf | 6 +++--- modules/nf-core/cnvkit/batch/meta.yml | 8 +++++--- modules/nf-core/cnvkit/call/main.nf | 6 +++--- modules/nf-core/cnvkit/call/meta.yml | 3 +++ modules/nf-core/cnvkit/export/main.nf | 6 +++--- modules/nf-core/cnvkit/export/meta.yml | 1 + modules/nf-core/cnvkit/genemetrics/main.nf | 6 +++--- modules/nf-core/cnvkit/genemetrics/meta.yml | 6 +++++- modules/nf-core/cnvkit/reference/main.nf | 6 +++--- modules/nf-core/cnvkit/reference/meta.yml | 2 ++ modules/nf-core/cnvkit/target/main.nf | 6 +++--- modules/nf-core/cnvkit/target/meta.yml | 1 + modules/nf-core/sequenzautils/bam2seqz/main.nf | 2 +- modules/nf-core/sequenzautils/bam2seqz/meta.yml | 2 ++ modules/nf-core/sequenzautils/gcwiggle/meta.yml | 2 ++ tests/modules/nf-core/cnvkit/batch/test.yml | 14 +++++++------- tests/modules/nf-core/cnvkit/export/test.yml | 5 +++-- tests/modules/nf-core/cnvkit/genemetrics/test.yml | 4 ++-- 22 files changed, 61 insertions(+), 40 deletions(-) diff --git a/modules/nf-core/cnvkit/access/main.nf b/modules/nf-core/cnvkit/access/main.nf index b99d4062259..496ef6dddbd 100644 --- a/modules/nf-core/cnvkit/access/main.nf +++ b/modules/nf-core/cnvkit/access/main.nf @@ -2,10 +2,10 @@ process CNVKIT_ACCESS { tag "$meta.id" label 'process_low' - conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1" + conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': - 'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0': + 'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/cnvkit/access/meta.yml b/modules/nf-core/cnvkit/access/meta.yml index 360902cfa66..7708841f40d 100644 --- a/modules/nf-core/cnvkit/access/meta.yml +++ b/modules/nf-core/cnvkit/access/meta.yml @@ -55,3 +55,4 @@ output: authors: - "@adamrtalbot" + - "@priesgo" diff --git a/modules/nf-core/cnvkit/antitarget/main.nf b/modules/nf-core/cnvkit/antitarget/main.nf index 9b19dc9dac8..cda05c635bd 100644 --- a/modules/nf-core/cnvkit/antitarget/main.nf +++ b/modules/nf-core/cnvkit/antitarget/main.nf @@ -2,10 +2,10 @@ process CNVKIT_ANTITARGET { tag "$meta.id" label 'process_low' - conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1" + conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': - 'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0': + 'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }" input: tuple val(meta), path(targets) diff --git a/modules/nf-core/cnvkit/antitarget/meta.yml b/modules/nf-core/cnvkit/antitarget/meta.yml index 378d0347d36..f22c07b13e2 100644 --- a/modules/nf-core/cnvkit/antitarget/meta.yml +++ b/modules/nf-core/cnvkit/antitarget/meta.yml @@ -43,4 +43,6 @@ output: pattern: "versions.yml" authors: + - "@adamrtalbot" + - "@priesgo" - "@SusiJo" diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf index 1e4d81e8a35..b253d6ab11e 100644 --- a/modules/nf-core/cnvkit/batch/main.nf +++ b/modules/nf-core/cnvkit/batch/main.nf @@ -2,10 +2,10 @@ process CNVKIT_BATCH { tag "$meta.id" label 'process_low' - conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1" + conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:3bdd798e4b9aed6d3e1aaa1596c913a3eeb865cb-0' : - 'biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:3bdd798e4b9aed6d3e1aaa1596c913a3eeb865cb-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:c94363856059151a2974dc501fb07a0360cc60a3-0' : + 'biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:c94363856059151a2974dc501fb07a0360cc60a3-0' }" input: tuple val(meta), path(tumor), path(normal) diff --git a/modules/nf-core/cnvkit/batch/meta.yml b/modules/nf-core/cnvkit/batch/meta.yml index 3fc00f1bfdb..950b0c9589a 100644 --- a/modules/nf-core/cnvkit/batch/meta.yml +++ b/modules/nf-core/cnvkit/batch/meta.yml @@ -77,10 +77,12 @@ output: description: File containing software versions pattern: "versions.yml" authors: - - "@kaurravneet4123" - - "@KevinMenden" - - "@MaxUlysse" + - "@adamrtalbot" - "@drpatelh" - "@fbdtemme" + - "@kaurravneet4123" + - "@KevinMenden" - "@lassefolkersen" + - "@MaxUlysse" + - "@priesgo" - "@SusiJo" diff --git a/modules/nf-core/cnvkit/call/main.nf b/modules/nf-core/cnvkit/call/main.nf index e79767c8ea8..8501cafedc2 100644 --- a/modules/nf-core/cnvkit/call/main.nf +++ b/modules/nf-core/cnvkit/call/main.nf @@ -2,10 +2,10 @@ process CNVKIT_CALL { tag "$meta.id" label 'process_single' - conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1" + conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': - 'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0': + 'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }" input: tuple val(meta) , path(cns), path(vcf) diff --git a/modules/nf-core/cnvkit/call/meta.yml b/modules/nf-core/cnvkit/call/meta.yml index 4bbec1f6475..52a20aad33c 100644 --- a/modules/nf-core/cnvkit/call/meta.yml +++ b/modules/nf-core/cnvkit/call/meta.yml @@ -2,6 +2,8 @@ name: cnvkit_call description: Given segmented log2 ratio estimates (.cns), derive each segment’s absolute integer copy number keywords: - cnvkit + - bam + - fasta - copy number tools: - cnvkit: @@ -47,3 +49,4 @@ output: authors: - "@adamrtalbot" + - "@priesgo" diff --git a/modules/nf-core/cnvkit/export/main.nf b/modules/nf-core/cnvkit/export/main.nf index 333d8589c92..fb77d30c5e0 100644 --- a/modules/nf-core/cnvkit/export/main.nf +++ b/modules/nf-core/cnvkit/export/main.nf @@ -2,10 +2,10 @@ process CNVKIT_EXPORT { tag "$meta.id" label 'process_single' - conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1" + conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': - 'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0': + 'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }" input: tuple val(meta) , path(cns) diff --git a/modules/nf-core/cnvkit/export/meta.yml b/modules/nf-core/cnvkit/export/meta.yml index a4359c9c34e..3617c73da4c 100644 --- a/modules/nf-core/cnvkit/export/meta.yml +++ b/modules/nf-core/cnvkit/export/meta.yml @@ -43,3 +43,4 @@ output: authors: - "@adamrtalbot" + - "@priesgo" diff --git a/modules/nf-core/cnvkit/genemetrics/main.nf b/modules/nf-core/cnvkit/genemetrics/main.nf index 109853cad47..60589948663 100755 --- a/modules/nf-core/cnvkit/genemetrics/main.nf +++ b/modules/nf-core/cnvkit/genemetrics/main.nf @@ -2,10 +2,10 @@ process CNVKIT_GENEMETRICS { tag "$meta.id" label 'process_low' - conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1" + conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': - 'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0': + 'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }" input: tuple val(meta), path(cnr), path(cns) diff --git a/modules/nf-core/cnvkit/genemetrics/meta.yml b/modules/nf-core/cnvkit/genemetrics/meta.yml index 1d8ee9e526f..115a4a87bbe 100755 --- a/modules/nf-core/cnvkit/genemetrics/meta.yml +++ b/modules/nf-core/cnvkit/genemetrics/meta.yml @@ -2,7 +2,9 @@ name: cnvkit_genemetrics description: Copy number variant detection from high-throughput sequencing data keywords: - cnvkit - - genemetrics + - bam + - fasta + - copy number tools: - cnvkit: description: | @@ -40,4 +42,6 @@ output: pattern: "versions.yml" authors: + - "@adamrtalbot" - "@marrip" + - "@priesgo" diff --git a/modules/nf-core/cnvkit/reference/main.nf b/modules/nf-core/cnvkit/reference/main.nf index fcefbadd42d..57e1aed4f01 100644 --- a/modules/nf-core/cnvkit/reference/main.nf +++ b/modules/nf-core/cnvkit/reference/main.nf @@ -2,10 +2,10 @@ process CNVKIT_REFERENCE { tag "$fasta" label 'process_low' - conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1" + conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': - 'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0': + 'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }" input: path fasta diff --git a/modules/nf-core/cnvkit/reference/meta.yml b/modules/nf-core/cnvkit/reference/meta.yml index f481c3c2338..eae82c75e79 100644 --- a/modules/nf-core/cnvkit/reference/meta.yml +++ b/modules/nf-core/cnvkit/reference/meta.yml @@ -46,4 +46,6 @@ output: pattern: "versions.yml" authors: + - "@adamrtalbot" + - "@priesgo" - "@SusiJo" diff --git a/modules/nf-core/cnvkit/target/main.nf b/modules/nf-core/cnvkit/target/main.nf index eda0eed5242..47d75ee24d6 100644 --- a/modules/nf-core/cnvkit/target/main.nf +++ b/modules/nf-core/cnvkit/target/main.nf @@ -2,10 +2,10 @@ process CNVKIT_TARGET { tag "$meta.id" label 'process_low' - conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1" + conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0': - 'biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0': + 'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }" input: tuple val(meta), path(baits) diff --git a/modules/nf-core/cnvkit/target/meta.yml b/modules/nf-core/cnvkit/target/meta.yml index 6d523587ae5..669af01e851 100644 --- a/modules/nf-core/cnvkit/target/meta.yml +++ b/modules/nf-core/cnvkit/target/meta.yml @@ -58,3 +58,4 @@ output: authors: - "@adamrtalbot" + - "@priesgo" diff --git a/modules/nf-core/sequenzautils/bam2seqz/main.nf b/modules/nf-core/sequenzautils/bam2seqz/main.nf index 1e5c136338d..46a89033b39 100644 --- a/modules/nf-core/sequenzautils/bam2seqz/main.nf +++ b/modules/nf-core/sequenzautils/bam2seqz/main.nf @@ -2,7 +2,7 @@ process SEQUENZAUTILS_BAM2SEQZ { tag "$meta.id" label 'process_medium' - conda "bioconda::sequenza-utils=3.0.0" + conda "bioconda::samtools=1.15.1 bioconda::sequenza-utils=3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2' : 'biocontainers/sequenza-utils:3.0.0--py38h6ed170a_2' }" diff --git a/modules/nf-core/sequenzautils/bam2seqz/meta.yml b/modules/nf-core/sequenzautils/bam2seqz/meta.yml index 0168bd68bfe..73dcdf740cc 100755 --- a/modules/nf-core/sequenzautils/bam2seqz/meta.yml +++ b/modules/nf-core/sequenzautils/bam2seqz/meta.yml @@ -1,6 +1,8 @@ name: sequenzautils_bam2seqz description: Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file keywords: + - sequenzautils + - copy number - bam2seqz tools: - sequenzautils: diff --git a/modules/nf-core/sequenzautils/gcwiggle/meta.yml b/modules/nf-core/sequenzautils/gcwiggle/meta.yml index 6e9a1483c2d..fa0b7bb0010 100644 --- a/modules/nf-core/sequenzautils/gcwiggle/meta.yml +++ b/modules/nf-core/sequenzautils/gcwiggle/meta.yml @@ -1,6 +1,8 @@ name: sequenzautils_gcwiggle description: Sequenza-utils gc_wiggle computes the GC percentage across the sequences, and returns a file in the UCSC wiggle format, given a fasta file and a window size. keywords: + - sequenzautils + - copy number - gc_wiggle tools: - sequenzautils: diff --git a/tests/modules/nf-core/cnvkit/batch/test.yml b/tests/modules/nf-core/cnvkit/batch/test.yml index 38f437f60e3..e57265d5d5c 100755 --- a/tests/modules/nf-core/cnvkit/batch/test.yml +++ b/tests/modules/nf-core/cnvkit/batch/test.yml @@ -12,7 +12,7 @@ - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn md5sum: 203caf8cef6935bb50b4138097955cb8 - path: output/cnvkit/test.paired_end.sorted.bintest.cns - md5sum: 6544d979475def8a9f69ba42a985668d + md5sum: b6701cceb525c3087f4dad432d20100c - path: output/cnvkit/test.paired_end.sorted.call.cns md5sum: f2ca59b4d50b0c317adc526c1b99b622 - path: output/cnvkit/test.paired_end.sorted.cnr @@ -46,7 +46,7 @@ - path: output/cnvkit/test2.paired_end.sorted.antitargetcoverage.cnn md5sum: 203caf8cef6935bb50b4138097955cb8 - path: output/cnvkit/test2.paired_end.sorted.bintest.cns - md5sum: 6544d979475def8a9f69ba42a985668d + md5sum: b6701cceb525c3087f4dad432d20100c - path: output/cnvkit/test2.paired_end.sorted.call.cns md5sum: f6de754c34f780e6befee5b3ff0893f8 - path: output/cnvkit/test2.paired_end.sorted.cnr @@ -76,7 +76,7 @@ - path: output/cnvkit/test2.paired_end.sorted.antitargetcoverage.cnn md5sum: 203caf8cef6935bb50b4138097955cb8 - path: output/cnvkit/test2.paired_end.sorted.bintest.cns - md5sum: 6544d979475def8a9f69ba42a985668d + md5sum: b6701cceb525c3087f4dad432d20100c - path: output/cnvkit/test2.paired_end.sorted.call.cns md5sum: f6de754c34f780e6befee5b3ff0893f8 - path: output/cnvkit/test2.paired_end.sorted.cnr @@ -99,7 +99,7 @@ - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn md5sum: 067115082c4af4b64d58c0dc3a3642e4 - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns - md5sum: f6adc75a0a86b7a921eca1b79a394cb0 + md5sum: 7a66b5f63acb05e6dfb0784c215851ec - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns md5sum: f7caeca04aba28b125ce26b511f42afb - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr @@ -122,7 +122,7 @@ - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn md5sum: 067115082c4af4b64d58c0dc3a3642e4 - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns - md5sum: f6adc75a0a86b7a921eca1b79a394cb0 + md5sum: 7a66b5f63acb05e6dfb0784c215851ec - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns md5sum: f7caeca04aba28b125ce26b511f42afb - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr @@ -147,7 +147,7 @@ - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn md5sum: 067115082c4af4b64d58c0dc3a3642e4 - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns - md5sum: 68b62b75cd91b2ffe5633686fb943490 + md5sum: 97ccb82da921185fcb033027914edf40 - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns md5sum: df196edd72613c59186f4d87df3dc4a4 - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr @@ -172,7 +172,7 @@ - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn md5sum: 067115082c4af4b64d58c0dc3a3642e4 - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns - md5sum: 68b62b75cd91b2ffe5633686fb943490 + md5sum: 97ccb82da921185fcb033027914edf40 - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns md5sum: df196edd72613c59186f4d87df3dc4a4 - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr diff --git a/tests/modules/nf-core/cnvkit/export/test.yml b/tests/modules/nf-core/cnvkit/export/test.yml index 96ce0866838..4f963a2f941 100644 --- a/tests/modules/nf-core/cnvkit/export/test.yml +++ b/tests/modules/nf-core/cnvkit/export/test.yml @@ -17,8 +17,9 @@ - path: output/cnvkit/test.vcf contains: - "##fileformat=VCFv4.2" - - "##source=CNVkit v0.9.9" - - "chr1\t160786623\t.\tN\t\t.\t.\tIMPRECISE;SVTYPE=DEL;END=160786747;SVLEN=-124;FOLD_CHANGE=0.271780;FOLD_CHANGE_LOG=-1.879490;PROBES=1\tGT:GQ\t0/1:1" + - "##source=CNVkit v0.9.10" + + - "chr1\t160786623\t.\tN\t\t.\t.\tIMPRECISE;SVTYPE=DEL;END=160786747;SVLEN=-124;FOLD_CHANGE=0.2717797741778673;FOLD_CHANGE_LOG=-1.87949;PROBES=1\tGT:GQ\t0/1:1" - path: output/cnvkit/versions.yml - name: cnvkit export test_cnvkit_export_cdt diff --git a/tests/modules/nf-core/cnvkit/genemetrics/test.yml b/tests/modules/nf-core/cnvkit/genemetrics/test.yml index 8df620e92c2..ac832836dde 100755 --- a/tests/modules/nf-core/cnvkit/genemetrics/test.yml +++ b/tests/modules/nf-core/cnvkit/genemetrics/test.yml @@ -7,7 +7,7 @@ - path: "output/cnvkit/test.tsv" md5sum: 2a18eca552ea33faab1d39795d9e051c - path: "output/cnvkit/versions.yml" - md5sum: 3d211e0077f86038ae454bdce8262cea + md5sum: 3158be0ead57ad4397444cdbe786994a - name: cnvkit genemetrics without cns command: nextflow run ./tests/modules/nf-core/cnvkit/genemetrics -entry test_cnvkit_genemetrics_without_cns -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cnvkit/genemetrics/nextflow.config @@ -18,4 +18,4 @@ - path: "output/cnvkit/test.tsv" md5sum: 622e154a107301da6f456b4b3196b79d - path: "output/cnvkit/versions.yml" - md5sum: dbc07d4b63731d5077845f9b53226260 + md5sum: 31293c53d7c9ef99bad1dc5b80929ee8 From 27902a200da5056a941cde0f15ec80878b5e837c Mon Sep 17 00:00:00 2001 From: "Thiseas C. Lamnidis" Date: Fri, 21 Jul 2023 15:15:40 +0200 Subject: [PATCH 3/3] Update gatk3 modules (#3660) * update mapdage2 module * Add meta for all files in gatk modules --- modules/nf-core/gatk/indelrealigner/main.nf | 8 ++-- modules/nf-core/gatk/indelrealigner/meta.yml | 20 +++++++++ .../gatk/realignertargetcreator/main.nf | 14 +++---- .../gatk/realignertargetcreator/meta.yml | 24 ++++++++++- modules/nf-core/gatk/unifiedgenotyper/main.nf | 18 ++++---- .../nf-core/gatk/unifiedgenotyper/meta.yml | 39 ++++++++++++++++- .../nf-core/gatk/indelrealigner/main.nf | 42 ++++++++++++------- .../gatk/realignertargetcreator/main.nf | 26 ++++++++---- .../nf-core/gatk/unifiedgenotyper/main.nf | 26 ++++++++---- 9 files changed, 161 insertions(+), 56 deletions(-) diff --git a/modules/nf-core/gatk/indelrealigner/main.nf b/modules/nf-core/gatk/indelrealigner/main.nf index 6a057ae8ef5..abcb245cabc 100644 --- a/modules/nf-core/gatk/indelrealigner/main.nf +++ b/modules/nf-core/gatk/indelrealigner/main.nf @@ -9,10 +9,10 @@ process GATK_INDELREALIGNER { input: tuple val(meta), path(bam), path(bai), path(intervals) - path(fasta) - path(fai) - path(dict) - path(known_vcf) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(dict) + tuple val(meta5), path(known_vcf) output: tuple val(meta), path("*.bam"), path("*.bai"), emit: bam diff --git a/modules/nf-core/gatk/indelrealigner/meta.yml b/modules/nf-core/gatk/indelrealigner/meta.yml index 35ad28e8e1f..6751f111703 100644 --- a/modules/nf-core/gatk/indelrealigner/meta.yml +++ b/modules/nf-core/gatk/indelrealigner/meta.yml @@ -31,18 +31,38 @@ input: type: file description: Intervals file created by gatk3 RealignerTargetCreator pattern: "*.{intervals,list}" + - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] - fasta: type: file description: Reference file used to generate BAM file pattern: ".{fasta,fa,fna}" + - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] - fai: type: file description: Index of reference file used to generate BAM file pattern: ".fai" + - meta4: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] - dict: type: file description: GATK dict file for reference pattern: ".dict" + - meta5: + type: map + description: | + Groovy Map containing file meta-information for known_vcf. + e.g. [ id:'test', single_end:false ] - known_vcf: type: file description: Optional input VCF file(s) with known indels diff --git a/modules/nf-core/gatk/realignertargetcreator/main.nf b/modules/nf-core/gatk/realignertargetcreator/main.nf index a4866417eb0..623ac468f7a 100644 --- a/modules/nf-core/gatk/realignertargetcreator/main.nf +++ b/modules/nf-core/gatk/realignertargetcreator/main.nf @@ -8,11 +8,11 @@ process GATK_REALIGNERTARGETCREATOR { 'biocontainers/gatk:3.5--hdfd78af_11' }" input: - tuple val(meta), path(input), path(index) - path fasta - path fai - path dict - path known_vcf + tuple val(meta), path(bam), path(bai) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(dict) + tuple val(meta5), path(known_vcf) output: tuple val(meta), path("*.intervals"), emit: intervals @@ -25,7 +25,7 @@ process GATK_REALIGNERTARGETCREATOR { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def known = known_vcf ? "-known ${known_vcf}" : "" - if ("$input" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!" + if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!" def avail_mem = 3072 if (!task.memory) { @@ -39,7 +39,7 @@ process GATK_REALIGNERTARGETCREATOR { -Xmx${avail_mem}M \\ -T RealignerTargetCreator \\ -nt ${task.cpus} \\ - -I ${input} \\ + -I ${bam} \\ -R ${fasta} \\ -o ${prefix}.intervals \\ ${known} \\ diff --git a/modules/nf-core/gatk/realignertargetcreator/meta.yml b/modules/nf-core/gatk/realignertargetcreator/meta.yml index c49d2a8d914..384c93e14a7 100644 --- a/modules/nf-core/gatk/realignertargetcreator/meta.yml +++ b/modules/nf-core/gatk/realignertargetcreator/meta.yml @@ -20,26 +20,46 @@ input: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - input: + - bam: type: file description: Sorted and indexed BAM/CRAM/SAM file pattern: "*.bam" - - index: + - bai: type: file description: BAM index file pattern: "*.bai" + - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] - fasta: type: file description: Reference file used to generate BAM file pattern: ".{fasta,fa,fna}" + - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] - fai: type: file description: Index of reference file used to generate BAM file pattern: ".fai" + - meta4: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] - dict: type: file description: GATK dict file for reference pattern: ".dict" + - meta5: + type: map + description: | + Groovy Map containing file meta-information for known_vcf. + e.g. [ id:'test', single_end:false ] - known_vcf: type: file description: Optional input VCF file(s) with known indels diff --git a/modules/nf-core/gatk/unifiedgenotyper/main.nf b/modules/nf-core/gatk/unifiedgenotyper/main.nf index fceb25e4871..99e700a33e6 100644 --- a/modules/nf-core/gatk/unifiedgenotyper/main.nf +++ b/modules/nf-core/gatk/unifiedgenotyper/main.nf @@ -8,14 +8,14 @@ process GATK_UNIFIEDGENOTYPER { 'biocontainers/gatk:3.5--hdfd78af_11' }" input: - tuple val(meta), path(input), path(index) - path fasta - path fai - path dict - path intervals - path contamination - path dbsnp - path comp + tuple val(meta), path(bam), path(bai) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(dict) + tuple val(meta5), path(intervals) + tuple val(meta6), path(contamination) + tuple val(meta7), path(dbsnp) + tuple val(meta8), path(comp) output: tuple val(meta), path("*.vcf.gz"), emit: vcf @@ -44,7 +44,7 @@ process GATK_UNIFIEDGENOTYPER { -Xmx${avail_mem}M \\ -nt ${task.cpus} \\ -T UnifiedGenotyper \\ - -I ${input} \\ + -I ${bam} \\ -R ${fasta} \\ ${contamination_file} \\ ${dbsnp_file} \\ diff --git a/modules/nf-core/gatk/unifiedgenotyper/meta.yml b/modules/nf-core/gatk/unifiedgenotyper/meta.yml index fc40bd6362c..f946411dff2 100644 --- a/modules/nf-core/gatk/unifiedgenotyper/meta.yml +++ b/modules/nf-core/gatk/unifiedgenotyper/meta.yml @@ -17,38 +17,73 @@ input: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - input: + - bam: type: file description: Sorted and indexed BAM/CRAM/SAM file pattern: "*.bam" - - index: + - bai: type: file description: BAM index file pattern: "*.bai" + - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] - fasta: type: file description: Reference file used to generate BAM file pattern: ".{fasta,fa,fna}" + - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] - fai: type: file description: Index of reference file used to generate BAM file pattern: ".fai" + - meta4: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] - dict: type: file description: GATK dict file for reference pattern: ".dict" + - meta5: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] - intervals: type: file description: Bed file with the genomic regions included in the library (optional) pattern: "*.intervals" + - meta6: + type: map + description: | + Groovy Map containing file meta-information for the contamination file. + e.g. [ id:'test', single_end:false ] - contamination: type: file description: Tab-separated file containing fraction of contamination in sequencing data (per sample) to aggressively remove pattern: "*" + - meta7: + type: map + description: | + Groovy Map containing file meta-information for the dbsnps file. + e.g. [ id:'test', single_end:false ] - dbsnps: type: file description: VCF file containing known sites (optional) pattern: "*" + - meta8: + type: map + description: | + Groovy Map containing file meta-information for the VCF comparison file. + e.g. [ id:'test', single_end:false ] - comp: type: file description: Comparison VCF file (optional) diff --git a/tests/modules/nf-core/gatk/indelrealigner/main.nf b/tests/modules/nf-core/gatk/indelrealigner/main.nf index 947c9d820c5..dcde7247517 100644 --- a/tests/modules/nf-core/gatk/indelrealigner/main.nf +++ b/tests/modules/nf-core/gatk/indelrealigner/main.nf @@ -8,26 +8,36 @@ include { GATK_INDELREALIGNER } from '../../../../../modules/nf-core/gatk/indelr workflow test_gatk_indelrealigner { - - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - - input_realignertargetcreator = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - ] - - GATK_REALIGNERTARGETCREATOR ( input_realignertargetcreator, fasta, fai, dict, [] ) + fasta = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + fai = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + ] + dict = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + ] + + input_realignertargetcreator = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + ] + + GATK_REALIGNERTARGETCREATOR ( input_realignertargetcreator, fasta, fai, dict, [[],[]] ) ch_intervals = GATK_REALIGNERTARGETCREATOR.out.intervals - ch_bams_indelrealigner = Channel.of([ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) - ]) + ch_bams_indelrealigner = Channel.of([ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + ]) ch_input_indelrealigner = ch_bams_indelrealigner.mix(ch_intervals).groupTuple(by: 0).map{ [it[0], it[1][0], it[2], it[1][1] ] } - GATK_INDELREALIGNER ( ch_input_indelrealigner, fasta, fai, dict, [] ) + GATK_INDELREALIGNER ( ch_input_indelrealigner, fasta, fai, dict, [[],[]] ) } diff --git a/tests/modules/nf-core/gatk/realignertargetcreator/main.nf b/tests/modules/nf-core/gatk/realignertargetcreator/main.nf index 9effbc9f80d..8eb4a27ab87 100644 --- a/tests/modules/nf-core/gatk/realignertargetcreator/main.nf +++ b/tests/modules/nf-core/gatk/realignertargetcreator/main.nf @@ -6,13 +6,23 @@ include { GATK_REALIGNERTARGETCREATOR } from '../../../../../modules/nf-core/gat workflow test_gatk_realignertargetcreator { - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + input = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + ] + fasta = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + fai = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + ] + dict = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + ] - GATK_REALIGNERTARGETCREATOR ( input, fasta, fai, dict, [] ) + GATK_REALIGNERTARGETCREATOR ( input, fasta, fai, dict, [[],[]] ) } diff --git a/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf b/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf index 9d7fc80904f..b308871657b 100644 --- a/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf +++ b/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf @@ -6,13 +6,23 @@ include { GATK_UNIFIEDGENOTYPER } from '../../../../../modules/nf-core/gatk/unif workflow test_gatk_unifiedgenotyper { - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + input = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + ] + fasta = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + fai = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + ] + dict = [ + [id: 'test'], + file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + ] - GATK_UNIFIEDGENOTYPER ( input, fasta, fai, dict, [], [], [], []) + GATK_UNIFIEDGENOTYPER ( input, fasta, fai, dict, [[],[]], [[],[]], [[],[]], [[],[]]) }