From 2f30bdf8b3c1f45788bf4a0ede849cb2a9d2f941 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 15 Aug 2023 14:19:19 +0000 Subject: [PATCH 01/21] Update modules --- modules.json | 52 +++++++++---------- modules/nf-core/bcftools/stats/main.nf | 14 +++-- modules/nf-core/bcftools/stats/meta.yml | 11 ++++ modules/nf-core/bwa/mem/main.nf | 12 +++++ 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/reference/main.nf | 6 +-- modules/nf-core/cnvkit/reference/meta.yml | 2 + .../nf-core/controlfreec/makegraph/main.nf | 4 +- .../nf-core/controlfreec/makegraph/meta.yml | 3 ++ modules/nf-core/deepvariant/main.nf | 13 +++-- modules/nf-core/ensemblvep/download/main.nf | 6 +-- modules/nf-core/ensemblvep/download/meta.yml | 8 +-- modules/nf-core/ensemblvep/vep/main.nf | 6 +-- modules/nf-core/fastqc/main.nf | 6 ++- modules/nf-core/gatk4/applybqsr/meta.yml | 1 + modules/nf-core/gatk4/applybqsrspark/main.nf | 4 +- modules/nf-core/gatk4/applyvqsr/main.nf | 12 +++++ .../nf-core/gatk4/cnnscorevariants/main.nf | 9 ++-- .../nf-core/gatk4/variantrecalibrator/main.nf | 14 +++++ modules/nf-core/mosdepth/main.nf | 4 +- modules/nf-core/sentieon/applyvarcal/main.nf | 4 +- modules/nf-core/sentieon/applyvarcal/meta.yml | 10 ++++ modules/nf-core/sentieon/bwamem/main.nf | 4 +- modules/nf-core/sentieon/bwamem/meta.yml | 10 ++++ modules/nf-core/sentieon/dedup/main.nf | 18 +++---- modules/nf-core/sentieon/dedup/meta.yml | 10 ++++ modules/nf-core/snpeff/download/meta.yml | 6 ++- modules/nf-core/snpeff/snpeff/main.nf | 2 +- modules/nf-core/snpeff/snpeff/meta.yml | 4 +- modules/nf-core/untar/main.nf | 2 +- modules/nf-core/unzip/main.nf | 2 +- modules/nf-core/unzip/meta.yml | 2 + .../nf-core/vcf_annotate_ensemblvep/meta.yml | 2 +- .../nf-core/vcf_annotate_snpeff/meta.yml | 3 +- 37 files changed, 201 insertions(+), 87 deletions(-) diff --git a/modules.json b/modules.json index fb43a04071..158b9887c6 100644 --- a/modules.json +++ b/modules.json @@ -27,7 +27,7 @@ }, "bcftools/stats": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "e2693a7e2d773b92e0649b25880ee22fe82bb79d", "installed_by": ["modules"] }, "bwa/index": { @@ -37,7 +37,7 @@ }, "bwa/mem": { "branch": "master", - "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220", + "git_sha": "3dc300ddcaa563c1e3503477557c0e0def6df2ce", "installed_by": ["modules"] }, "bwamem2/index": { @@ -62,17 +62,17 @@ }, "cnvkit/antitarget": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3b63e1df297ef474b0070aa5fabb30d732173671", "installed_by": ["modules"] }, "cnvkit/batch": { "branch": "master", - "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220", + "git_sha": "3b63e1df297ef474b0070aa5fabb30d732173671", "installed_by": ["modules"] }, "cnvkit/reference": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3b63e1df297ef474b0070aa5fabb30d732173671", "installed_by": ["modules"] }, "controlfreec/assesssignificance": { @@ -97,7 +97,7 @@ }, "controlfreec/makegraph": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "83ddd598664e16f74e0b5c728e9f81285c37e893", "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { @@ -107,7 +107,7 @@ }, "deepvariant": { "branch": "master", - "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b", + "git_sha": "ed67f2fadd6d2a155b296f728e6b1f8c92ddc1a6", "installed_by": ["modules"] }, "dragmap/align": { @@ -123,13 +123,13 @@ }, "ensemblvep/download": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "9f9e1fc31cb35876922070c0e601ae05abae5cae", "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": ["vcf_annotate_ensemblvep", "modules"] + "git_sha": "9f9e1fc31cb35876922070c0e601ae05abae5cae", + "installed_by": ["modules", "vcf_annotate_ensemblvep"] }, "fastp": { "branch": "master", @@ -138,7 +138,7 @@ }, "fastqc": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117", "installed_by": ["modules"] }, "fgbio/callmolecularconsensusreads": { @@ -163,17 +163,17 @@ }, "gatk4/applybqsr": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "240937a2a9c30298110753292be041188891f2cb", "installed_by": ["modules"] }, "gatk4/applybqsrspark": { "branch": "master", - "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b", + "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117", "installed_by": ["modules"] }, "gatk4/applyvqsr": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "359dcb06bda60c43955752e356e25c91cfd38ae0", "installed_by": ["modules"] }, "gatk4/baserecalibrator": { @@ -193,7 +193,7 @@ }, "gatk4/cnnscorevariants": { "branch": "master", - "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b", + "git_sha": "8c4542e5d421c4690cf1fa6ec729e9304763fdaf", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { @@ -283,7 +283,7 @@ }, "gatk4/variantrecalibrator": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "359dcb06bda60c43955752e356e25c91cfd38ae0", "installed_by": ["modules"] }, "manta/germline": { @@ -303,7 +303,7 @@ }, "mosdepth": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "ebb27711cd5f4de921244bfa81c676504072d31c", "installed_by": ["modules"] }, "msisensorpro/msi_somatic": { @@ -373,17 +373,17 @@ }, "sentieon/applyvarcal": { "branch": "master", - "git_sha": "b9172e8c26a3db5009f7872654c44587e254f094", + "git_sha": "0ff77bd14d74332f4f0aaecfb302c51a9b24231a", "installed_by": ["modules"] }, "sentieon/bwamem": { "branch": "master", - "git_sha": "b9172e8c26a3db5009f7872654c44587e254f094", + "git_sha": "149b4746c6e16ef84f64db5bb245d5b9495fdc3f", "installed_by": ["modules"] }, "sentieon/dedup": { "branch": "master", - "git_sha": "b9172e8c26a3db5009f7872654c44587e254f094", + "git_sha": "915a0b16ba3e40ef59e7b44843b3118e17a9c906", "installed_by": ["modules"] }, "sentieon/gvcftyper": { @@ -403,12 +403,12 @@ }, "snpeff/download": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "4d584d5cf6ed5f7363a51cdb4b3eb25398e9e537", "installed_by": ["modules"] }, "snpeff/snpeff": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "4d584d5cf6ed5f7363a51cdb4b3eb25398e9e537", "installed_by": ["vcf_annotate_snpeff", "modules"] }, "strelka/germline": { @@ -443,12 +443,12 @@ }, "untar": { "branch": "master", - "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e", + "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8", "installed_by": ["modules"] }, "unzip": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "cf67a6d7d043e2bd6a3099be84c72046fc71508f", "installed_by": ["modules"] }, "vcftools": { @@ -462,12 +462,12 @@ "nf-core": { "vcf_annotate_ensemblvep": { "branch": "master", - "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653", + "git_sha": "dedc0e31087f3306101c38835d051bf49789445a", "installed_by": ["subworkflows"] }, "vcf_annotate_snpeff": { "branch": "master", - "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653", + "git_sha": "dedc0e31087f3306101c38835d051bf49789445a", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf index 46ce4ba64d..7ccb9bf6cb 100644 --- a/modules/nf-core/bcftools/stats/main.nf +++ b/modules/nf-core/bcftools/stats/main.nf @@ -8,10 +8,12 @@ process BCFTOOLS_STATS { 'biocontainers/bcftools:1.17--haef29d1_0' }" input: - tuple val(meta), path(vcf), path(tbi) - path regions - path targets - path samples + tuple val(meta), path(vcf), path(tbi) + tuple val(meta2), path(regions) + tuple val(meta3), path(targets) + tuple val(meta4), path(samples) + tuple val(meta5), path(exons) + tuple val(meta6), path(fasta) output: tuple val(meta), path("*stats.txt"), emit: stats @@ -26,12 +28,16 @@ process BCFTOOLS_STATS { def regions_file = regions ? "--regions-file ${regions}" : "" def targets_file = targets ? "--targets-file ${targets}" : "" def samples_file = samples ? "--samples-file ${samples}" : "" + def reference_fasta = fasta ? "--fasta-ref ${fasta}" : "" + def exons_file = exons ? "--exons ${exons}" : "" """ bcftools stats \\ $args \\ $regions_file \\ $targets_file \\ $samples_file \\ + $reference_fasta \\ + $exons_file \\ $vcf > ${prefix}.bcftools_stats.txt cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/bcftools/stats/meta.yml b/modules/nf-core/bcftools/stats/meta.yml index f7afcd5093..5850d25f71 100644 --- a/modules/nf-core/bcftools/stats/meta.yml +++ b/modules/nf-core/bcftools/stats/meta.yml @@ -41,6 +41,16 @@ input: description: | Optional, file of sample names to be included or excluded. e.g. 'file.tsv' + - exons: + type: file + description: | + Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed). + e.g. 'exons.tsv.gz' + - fasta: + type: file + description: | + Faidx indexed reference sequence file to determine INDEL context. + e.g. 'reference.fa' output: - meta: type: map @@ -59,3 +69,4 @@ authors: - "@joseespinosa" - "@drpatelh" - "@SusiJo" + - "@TCLamnidis" diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index d2f85dafeb..8ba99dfdb7 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -40,4 +40,16 @@ process BWA_MEM { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/cnvkit/antitarget/main.nf b/modules/nf-core/cnvkit/antitarget/main.nf index 9b19dc9dac..cda05c635b 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 378d0347d3..f22c07b13e 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 1e4d81e8a3..b253d6ab11 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 3fc00f1bfd..950b0c9589 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/reference/main.nf b/modules/nf-core/cnvkit/reference/main.nf index fcefbadd42..57e1aed4f0 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 f481c3c233..eae82c75e7 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/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf index 293cf1feaa..91231ad8c7 100644 --- a/modules/nf-core/controlfreec/makegraph/main.nf +++ b/modules/nf-core/controlfreec/makegraph/main.nf @@ -8,7 +8,7 @@ process CONTROLFREEC_MAKEGRAPH { 'biocontainers/control-freec:11.6--h1b792b2_1' }" input: - tuple val(meta), path(ratio), path(baf) + tuple val(meta), path(ratio), path(baf), val(ploidy) output: tuple val(meta), path("*_BAF.png") , emit: png_baf @@ -25,7 +25,7 @@ process CONTROLFREEC_MAKEGRAPH { def prefix = task.ext.prefix ?: "${meta.id}" def baf = baf ?: "" """ - cat \$(which makeGraph.R) | R --slave --args ${args} ${ratio} ${baf} + cat \$(which makeGraph.R) | R --slave --args ${ploidy} ${args} ${ratio} ${baf} mv *_BAF.txt.png ${prefix}_BAF.png mv *_ratio.txt.log2.png ${prefix}_ratio.log2.png diff --git a/modules/nf-core/controlfreec/makegraph/meta.yml b/modules/nf-core/controlfreec/makegraph/meta.yml index a207ec8c8f..7b97dcf9bc 100644 --- a/modules/nf-core/controlfreec/makegraph/meta.yml +++ b/modules/nf-core/controlfreec/makegraph/meta.yml @@ -30,6 +30,9 @@ input: type: file description: .BAF file generated by FREEC pattern: "*.BAF" + - ploidy: + type: integer + description: Ploidy value for which graph should be created output: - meta: diff --git a/modules/nf-core/deepvariant/main.nf b/modules/nf-core/deepvariant/main.nf index 1a24ba34b8..2d5c480c4d 100644 --- a/modules/nf-core/deepvariant/main.nf +++ b/modules/nf-core/deepvariant/main.nf @@ -4,11 +4,6 @@ process DEEPVARIANT { container "nf-core/deepvariant:1.5.0" - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: tuple val(meta), path(input), path(index), path(intervals) tuple val(meta2), path(fasta) @@ -26,6 +21,10 @@ process DEEPVARIANT { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def regions = intervals ? "--regions=${intervals}" : "" @@ -48,6 +47,10 @@ process DEEPVARIANT { """ stub: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead." + } prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.vcf.gz diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf index ba3ef8872f..4873b91d57 100644 --- a/modules/nf-core/ensemblvep/download/main.nf +++ b/modules/nf-core/ensemblvep/download/main.nf @@ -2,10 +2,10 @@ process ENSEMBLVEP_DOWNLOAD { tag "$meta.id" label 'process_medium' - conda "bioconda::ensembl-vep=108.2" + conda "bioconda::ensembl-vep=110.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:108.2--pl5321h4a94de4_0' : - 'biocontainers/ensembl-vep:108.2--pl5321h4a94de4_0' }" + 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : + 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }" input: tuple val(meta), val(assembly), val(species), val(cache_version) diff --git a/modules/nf-core/ensemblvep/download/meta.yml b/modules/nf-core/ensemblvep/download/meta.yml index ae84937d3c..acb337c399 100644 --- a/modules/nf-core/ensemblvep/download/meta.yml +++ b/modules/nf-core/ensemblvep/download/meta.yml @@ -2,6 +2,8 @@ name: ENSEMBLVEP_DOWNLOAD description: Ensembl Variant Effect Predictor (VEP). The cache downloading options are controlled through `task.ext.args`. keywords: - annotation + - cache + - download tools: - ensemblvep: description: | @@ -17,15 +19,15 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - assembly: - type: value + type: string description: | Genome assembly - species: - type: value + type: string description: | Specie - cache_version: - type: value + type: string description: | cache version output: diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index 2db61dc90e..da0e36460a 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -2,10 +2,10 @@ process ENSEMBLVEP_VEP { tag "$meta.id" label 'process_medium' - conda "bioconda::ensembl-vep=108.2" + conda "bioconda::ensembl-vep=110.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:108.2--pl5321h4a94de4_0' : - 'biocontainers/ensembl-vep:108.2--pl5321h4a94de4_0' }" + 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : + 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }" input: tuple val(meta), path(vcf), path(custom_extra_files) diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 07d5e43312..249f90644d 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -29,7 +29,11 @@ process FASTQC { printf "%s %s\\n" $rename_to | while read old_name new_name; do [ -f "\${new_name}" ] || ln -s \$old_name \$new_name done - fastqc $args --threads $task.cpus $renamed_files + + fastqc \\ + $args \\ + --threads $task.cpus \\ + $renamed_files cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/gatk4/applybqsr/meta.yml b/modules/nf-core/gatk4/applybqsr/meta.yml index c7255bff86..3002ab600e 100644 --- a/modules/nf-core/gatk4/applybqsr/meta.yml +++ b/modules/nf-core/gatk4/applybqsr/meta.yml @@ -3,6 +3,7 @@ description: Apply base quality score recalibration (BQSR) to a bam file keywords: - bqsr - bam + - base quality score recalibration tools: - gatk4: description: | diff --git a/modules/nf-core/gatk4/applybqsrspark/main.nf b/modules/nf-core/gatk4/applybqsrspark/main.nf index 88ead471c8..6451b1bad4 100644 --- a/modules/nf-core/gatk4/applybqsrspark/main.nf +++ b/modules/nf-core/gatk4/applybqsrspark/main.nf @@ -31,7 +31,9 @@ process GATK4_APPLYBQSR_SPARK { avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}M" ApplyBQSRSpark \\ + gatk \\ + --java-options "-Xmx${avail_mem}M" \\ + ApplyBQSRSpark \\ --input $input \\ --output ${prefix}.${input.getExtension()} \\ --reference $fasta \\ diff --git a/modules/nf-core/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf index 06010cc29f..381af40fb1 100644 --- a/modules/nf-core/gatk4/applyvqsr/main.nf +++ b/modules/nf-core/gatk4/applyvqsr/main.nf @@ -47,4 +47,16 @@ process GATK4_APPLYVQSR { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.vcf.gz + touch ${prefix}.vcf.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/cnnscorevariants/main.nf b/modules/nf-core/gatk4/cnnscorevariants/main.nf index 5e843ce6c6..25e476411f 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/main.nf +++ b/modules/nf-core/gatk4/cnnscorevariants/main.nf @@ -5,11 +5,6 @@ process GATK4_CNNSCOREVARIANTS { //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 container "nf-core/gatk:4.4.0.0" //Biocontainers is missing a package - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "GATK4_CNNSCOREVARIANTS module does not support Conda. Please use Docker / Singularity / Podman instead." - } - input: tuple val(meta), path(vcf), path(tbi), path(aligned_input), path(intervals) path fasta @@ -27,6 +22,10 @@ process GATK4_CNNSCOREVARIANTS { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "GATK4_CNNSCOREVARIANTS module does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def aligned_input = aligned_input ? "--input $aligned_input" : "" diff --git a/modules/nf-core/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf index 6b4c2ece71..adfd1063ed 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/main.nf +++ b/modules/nf-core/gatk4/variantrecalibrator/main.nf @@ -53,4 +53,18 @@ process GATK4_VARIANTRECALIBRATOR { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.recal + touch ${prefix}.idx + touch ${prefix}.tranches + touch ${prefix}plots.R + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index c17e4e658e..74db3a274b 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -35,10 +35,10 @@ process MOSDEPTH { def reference = fasta ? "--fasta ${fasta}" : "" def interval = bed ? "--by ${bed}" : "" if (bed && args.contains("--by")) { - exit 1, "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition" + error "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition" } if (!bed && args.contains("--thresholds")) { - exit 1, "'--thresholds' can only be specified in conjunction with '--by'" + error "'--thresholds' can only be specified in conjunction with '--by'" } """ diff --git a/modules/nf-core/sentieon/applyvarcal/main.nf b/modules/nf-core/sentieon/applyvarcal/main.nf index 1dc3883ded..98b7c88576 100644 --- a/modules/nf-core/sentieon/applyvarcal/main.nf +++ b/modules/nf-core/sentieon/applyvarcal/main.nf @@ -9,8 +9,8 @@ process SENTIEON_APPLYVARCAL { input: tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches) - path fasta - path fai + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) output: tuple val(meta), path("*.vcf.gz"), emit: vcf diff --git a/modules/nf-core/sentieon/applyvarcal/meta.yml b/modules/nf-core/sentieon/applyvarcal/meta.yml index 0067dd3d8d..bbe23ea375 100644 --- a/modules/nf-core/sentieon/applyvarcal/meta.yml +++ b/modules/nf-core/sentieon/applyvarcal/meta.yml @@ -44,10 +44,20 @@ input: type: file description: Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1. pattern: ".tranches" + - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] - fasta: type: file description: The reference fasta file pattern: "*.fasta" + - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] - fai: type: file description: Index of reference fasta file diff --git a/modules/nf-core/sentieon/bwamem/main.nf b/modules/nf-core/sentieon/bwamem/main.nf index aeca282560..b58835fda5 100644 --- a/modules/nf-core/sentieon/bwamem/main.nf +++ b/modules/nf-core/sentieon/bwamem/main.nf @@ -10,8 +10,8 @@ process SENTIEON_BWAMEM { input: tuple val(meta), path(reads) tuple val(meta2), path(index) - path(fasta) - path(fasta_fai) + tuple val(meta3), path(fasta) + tuple val(meta4), path(fasta_fai) output: tuple val(meta), path("*.bam"), path("*.bai"), emit: bam_and_bai diff --git a/modules/nf-core/sentieon/bwamem/meta.yml b/modules/nf-core/sentieon/bwamem/meta.yml index 3d1546c55d..9987e8c900 100644 --- a/modules/nf-core/sentieon/bwamem/meta.yml +++ b/modules/nf-core/sentieon/bwamem/meta.yml @@ -33,10 +33,20 @@ input: type: file description: BWA genome index files pattern: "*.{amb,ann,bwt,pac,sa}" + - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] - fasta: type: file description: Genome fasta file pattern: "*.{fa,fasta}" + - meta4: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] - fasta_fai: type: file description: The index of the FASTA reference. diff --git a/modules/nf-core/sentieon/dedup/main.nf b/modules/nf-core/sentieon/dedup/main.nf index faa14fe011..c83d5e552a 100644 --- a/modules/nf-core/sentieon/dedup/main.nf +++ b/modules/nf-core/sentieon/dedup/main.nf @@ -9,18 +9,18 @@ process SENTIEON_DEDUP { input: tuple val(meta), path(bam), path(bai) - path fasta - path fasta_fai + tuple val(meta2), path(fasta) + tuple val(meta3), path(fasta_fai) output: - tuple val(meta), path("*.cram"), emit: cram, optional: true - tuple val(meta), path("*.crai"), emit: crai, optional: true - tuple val(meta), path("*.bam"), emit: bam, optional: true - tuple val(meta), path("*.bai"), emit: bai - tuple val(meta), path("*.score"), emit: score - tuple val(meta), path("*.metrics"), emit: metrics + tuple val(meta), path("*.cram") , emit: cram, optional: true + tuple val(meta), path("*.crai") , emit: crai, optional: true + tuple val(meta), path("*.bam") , emit: bam , optional: true + tuple val(meta), path("*.bai") , emit: bai + tuple val(meta), path("*.score") , emit: score + tuple val(meta), path("*.metrics") , emit: metrics tuple val(meta), path("*.metrics.multiqc.tsv"), emit: metrics_multiqc_tsv - path "versions.yml", emit: versions + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/sentieon/dedup/meta.yml b/modules/nf-core/sentieon/dedup/meta.yml index 6813d663bc..ec0565d923 100644 --- a/modules/nf-core/sentieon/dedup/meta.yml +++ b/modules/nf-core/sentieon/dedup/meta.yml @@ -28,10 +28,20 @@ input: type: file description: BAI file pattern: "*.bai" + - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] - fasta: type: file description: Genome fasta file pattern: "*.{fa,fasta}" + - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] - fasta_fai: type: file description: The index of the FASTA reference. diff --git a/modules/nf-core/snpeff/download/meta.yml b/modules/nf-core/snpeff/download/meta.yml index 07a7afaf8b..3c03c2f602 100644 --- a/modules/nf-core/snpeff/download/meta.yml +++ b/modules/nf-core/snpeff/download/meta.yml @@ -2,6 +2,10 @@ name: SNPEFF_DOWNLOAD description: Genetic variant annotation and functional effect prediction toolbox keywords: - annotation + - effect prediction + - snpeff + - variant + - vcf tools: - snpeff: description: | @@ -21,7 +25,7 @@ input: description: | vcf to annotate - db: - type: value + type: string description: | which db to annotate with output: diff --git a/modules/nf-core/snpeff/snpeff/main.nf b/modules/nf-core/snpeff/snpeff/main.nf index 84f5ee5d58..e92c1597e7 100644 --- a/modules/nf-core/snpeff/snpeff/main.nf +++ b/modules/nf-core/snpeff/snpeff/main.nf @@ -10,7 +10,7 @@ process SNPEFF_SNPEFF { input: tuple val(meta), path(vcf) val db - path cache + tuple val(meta2), path(cache) output: tuple val(meta), path("*.ann.vcf"), emit: vcf diff --git a/modules/nf-core/snpeff/snpeff/meta.yml b/modules/nf-core/snpeff/snpeff/meta.yml index cf00c819ac..44bada2303 100644 --- a/modules/nf-core/snpeff/snpeff/meta.yml +++ b/modules/nf-core/snpeff/snpeff/meta.yml @@ -2,8 +2,10 @@ name: SNPEFF_SNPEFF description: Genetic variant annotation and functional effect prediction toolbox keywords: - annotation - - variant - effect prediction + - snpeff + - variant + - vcf tools: - snpeff: description: | diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 8cd1856c71..61461c3917 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -2,7 +2,7 @@ process UNTAR { tag "$archive" label 'process_single' - conda "conda-forge::sed=4.7 bioconda::grep=3.4 conda-forge::tar=1.34" + conda "conda-forge::sed=4.7 conda-forge::grep=3.11 conda-forge::tar=1.34" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf index f9617ad5f2..cf977f1dcb 100644 --- a/modules/nf-core/unzip/main.nf +++ b/modules/nf-core/unzip/main.nf @@ -19,7 +19,7 @@ process UNZIP { script: def args = task.ext.args ?: '' - if ( archive instanceof List && archive.name.size > 1 ) { exit 1, "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." } + if ( archive instanceof List && archive.name.size > 1 ) { error "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." } prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName) """ diff --git a/modules/nf-core/unzip/meta.yml b/modules/nf-core/unzip/meta.yml index f924bfb4f1..2910e0fd3f 100644 --- a/modules/nf-core/unzip/meta.yml +++ b/modules/nf-core/unzip/meta.yml @@ -3,6 +3,8 @@ description: Unzip ZIP archive files keywords: - unzip - decompression + - zip + - archiving tools: - unzip: description: p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org) for Unix. diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep/meta.yml b/subworkflows/nf-core/vcf_annotate_ensemblvep/meta.yml index 2f7d2191fb..7a9fd10c4e 100644 --- a/subworkflows/nf-core/vcf_annotate_ensemblvep/meta.yml +++ b/subworkflows/nf-core/vcf_annotate_ensemblvep/meta.yml @@ -5,7 +5,7 @@ keywords: - vcf - annotation - ensemblvep -modules: +components: - ensemblvep/vep - tabix/tabix input: diff --git a/subworkflows/nf-core/vcf_annotate_snpeff/meta.yml b/subworkflows/nf-core/vcf_annotate_snpeff/meta.yml index 0c0c94b535..b3f10cae12 100644 --- a/subworkflows/nf-core/vcf_annotate_snpeff/meta.yml +++ b/subworkflows/nf-core/vcf_annotate_snpeff/meta.yml @@ -5,8 +5,9 @@ keywords: - vcf - annotation - snpeff -modules: +components: - snpeff + - snpeff/snpeff - tabix/bgziptabix input: - ch_vcf: From 0dce1c09b48e38dfdd60198f61fe54205abd0f3f Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 15 Aug 2023 14:32:47 +0000 Subject: [PATCH 02/21] Add required input channels for bcftools_stats --- subworkflows/local/vcf_qc_bcftools_vcftools/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/vcf_qc_bcftools_vcftools/main.nf b/subworkflows/local/vcf_qc_bcftools_vcftools/main.nf index 55fbf59bd9..c6dd43e1db 100644 --- a/subworkflows/local/vcf_qc_bcftools_vcftools/main.nf +++ b/subworkflows/local/vcf_qc_bcftools_vcftools/main.nf @@ -12,7 +12,7 @@ workflow VCF_QC_BCFTOOLS_VCFTOOLS { versions = Channel.empty() - BCFTOOLS_STATS(vcf.map{ meta, vcf -> [ meta, vcf, [] ] }, [], [], []) + BCFTOOLS_STATS(vcf.map{ meta, vcf -> [ meta, vcf, [] ] }, [], [], [], [], []) VCFTOOLS_TSTV_COUNT(vcf, target_bed, []) VCFTOOLS_TSTV_QUAL(vcf, target_bed, []) VCFTOOLS_SUMMARY(vcf, target_bed, []) From 2e02a1ca70cec6bc2fafa249c63f9cdb4b442d72 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 15 Aug 2023 14:48:12 +0000 Subject: [PATCH 03/21] Trying to fix call to SENTIEON_BWAMEM --- .../local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf b/subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf index 914cf55ec2..d5140081be 100644 --- a/subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf +++ b/subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf @@ -26,7 +26,7 @@ workflow FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON { BWAMEM1_MEM(reads, index.map{ it -> [ [ id:'index' ], it ] }, sort) // If aligner is bwa-mem BWAMEM2_MEM(reads, index.map{ it -> [ [ id:'index' ], it ] }, sort) // If aligner is bwa-mem2 DRAGMAP_ALIGN(reads, index.map{ it -> [ [ id:'index' ], it ] }, sort) // If aligner is dragmap - SENTIEON_BWAMEM(reads, index.map{ it -> [ [ id:'index' ], it ] }, fasta, fasta_fai) // The sentieon-bwamem-module does sorting as part of the conversion from sam to bam. + SENTIEON_BWAMEM(reads, index.map{ it -> [ [ id:'index' ], it ] }, [[:], fasta], [[:], fasta_fai]) // The sentieon-bwamem-module does sorting as part of the conversion from sam to bam. // Get the bam files from the aligner // Only one aligner is run From 3c69795862953b76b200d055faa21579e78fb147 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 15 Aug 2023 15:01:09 +0000 Subject: [PATCH 04/21] Trying to fix call to SENTIEON_BWAMEM --- .../local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf b/subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf index d5140081be..c61ac7f4cc 100644 --- a/subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf +++ b/subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf @@ -26,7 +26,8 @@ workflow FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON { BWAMEM1_MEM(reads, index.map{ it -> [ [ id:'index' ], it ] }, sort) // If aligner is bwa-mem BWAMEM2_MEM(reads, index.map{ it -> [ [ id:'index' ], it ] }, sort) // If aligner is bwa-mem2 DRAGMAP_ALIGN(reads, index.map{ it -> [ [ id:'index' ], it ] }, sort) // If aligner is dragmap - SENTIEON_BWAMEM(reads, index.map{ it -> [ [ id:'index' ], it ] }, [[:], fasta], [[:], fasta_fai]) // The sentieon-bwamem-module does sorting as part of the conversion from sam to bam. + // The sentieon-bwamem-module does sorting as part of the conversion from sam to bam. + SENTIEON_BWAMEM(reads, index.map{ it -> [ [ id:'index' ], it ] }, fasta.map{fa -> [[:], fa]}, fasta_fai.map{fai -> [[:], fai]}) // If aligner is sentieon-bwamem // Get the bam files from the aligner // Only one aligner is run From 95e9cbb609527bb53ee0797b3c0c9fa84a253782 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 15 Aug 2023 20:07:50 +0000 Subject: [PATCH 05/21] Trying to input-channels for BCFTOOLS_STATS right --- subworkflows/local/vcf_qc_bcftools_vcftools/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/vcf_qc_bcftools_vcftools/main.nf b/subworkflows/local/vcf_qc_bcftools_vcftools/main.nf index c6dd43e1db..bcdc34e30d 100644 --- a/subworkflows/local/vcf_qc_bcftools_vcftools/main.nf +++ b/subworkflows/local/vcf_qc_bcftools_vcftools/main.nf @@ -12,7 +12,7 @@ workflow VCF_QC_BCFTOOLS_VCFTOOLS { versions = Channel.empty() - BCFTOOLS_STATS(vcf.map{ meta, vcf -> [ meta, vcf, [] ] }, [], [], [], [], []) + BCFTOOLS_STATS(vcf.map{ meta, vcf -> [ meta, vcf, [] ] }, [[:],[]], [[:],[]], [[:],[]], [[:],[]], [[:],[]]) VCFTOOLS_TSTV_COUNT(vcf, target_bed, []) VCFTOOLS_TSTV_QUAL(vcf, target_bed, []) VCFTOOLS_SUMMARY(vcf, target_bed, []) From f2886867767a4d8a360ff24cc5f67acc8a4e8dd3 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 15 Aug 2023 20:23:37 +0000 Subject: [PATCH 06/21] Fix input-channels for SENTIEON_DEDUP --- subworkflows/local/bam_sentieon_dedup/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/bam_sentieon_dedup/main.nf b/subworkflows/local/bam_sentieon_dedup/main.nf index e068573234..a60b12b931 100644 --- a/subworkflows/local/bam_sentieon_dedup/main.nf +++ b/subworkflows/local/bam_sentieon_dedup/main.nf @@ -22,7 +22,7 @@ workflow BAM_SENTIEON_DEDUP { bam = bam.map{ meta, bam -> [ meta - meta.subMap('data_type'), bam ] } bai = bai.map{ meta, bai -> [ meta - meta.subMap('data_type'), bai ] } bam_bai = bam.join(bai, failOnMismatch:true, failOnDuplicate:true) - SENTIEON_DEDUP(bam_bai, fasta, fasta_fai) + SENTIEON_DEDUP(bam_bai, fasta.map{fa -> [[:], fa]}, fasta_fai.map{fai -> [[:], fai]}) // Join with the crai file cram = SENTIEON_DEDUP.out.cram.join(SENTIEON_DEDUP.out.crai, failOnDuplicate: true, failOnMismatch: true) From 409adb8d34bdf3081d64476b4187096d4fca609b Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 15 Aug 2023 21:08:23 +0000 Subject: [PATCH 07/21] Trying to fix input-channels for SNPEFF_SNPEFF --- subworkflows/nf-core/vcf_annotate_snpeff/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/nf-core/vcf_annotate_snpeff/main.nf b/subworkflows/nf-core/vcf_annotate_snpeff/main.nf index 3570a5b7c0..2f37454d17 100644 --- a/subworkflows/nf-core/vcf_annotate_snpeff/main.nf +++ b/subworkflows/nf-core/vcf_annotate_snpeff/main.nf @@ -14,7 +14,7 @@ workflow VCF_ANNOTATE_SNPEFF { main: ch_versions = Channel.empty() - SNPEFF_SNPEFF(ch_vcf, val_snpeff_db, ch_snpeff_cache) + SNPEFF_SNPEFF(ch_vcf, val_snpeff_db, ch_snpeff_cache.map{it -> [[:], it]}) TABIX_BGZIPTABIX(SNPEFF_SNPEFF.out.vcf) // Gather versions of all tools used From 64ca3f38532a39e77e35c8c055b24ba631442dc2 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 15 Aug 2023 21:51:46 +0000 Subject: [PATCH 08/21] Trying to handle Missing process or function map related to VCF_ANNOTATE_SNPEFF --- workflows/sarek.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 669dac1bd5..fa93989d30 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -312,7 +312,7 @@ vep_genome = params.vep_genome ?: Channel.empty() vep_species = params.vep_species ?: Channel.empty() // Initialize files channels based on params, not defined within the params.genomes[params.genome] scope -snpeff_cache = params.snpeff_cache ? Channel.fromPath(params.snpeff_cache).collect() : [] +snpeff_cache = params.snpeff_cache ? Channel.fromPath(params.snpeff_cache).collect() : Channel.empty() vep_cache = params.vep_cache ? Channel.fromPath(params.vep_cache).collect() : [] vep_extra_files = [] From 7cdea7c0a417aaec63494c13714bc3ce15051dcd Mon Sep 17 00:00:00 2001 From: asp8200 Date: Wed, 16 Aug 2023 07:19:15 +0000 Subject: [PATCH 09/21] Trying to get call to SNPEFF to work --- workflows/sarek.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/sarek.nf b/workflows/sarek.nf index fa93989d30..70a59ecaf3 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -312,7 +312,7 @@ vep_genome = params.vep_genome ?: Channel.empty() vep_species = params.vep_species ?: Channel.empty() // Initialize files channels based on params, not defined within the params.genomes[params.genome] scope -snpeff_cache = params.snpeff_cache ? Channel.fromPath(params.snpeff_cache).collect() : Channel.empty() +snpeff_cache = params.snpeff_cache ? Channel.fromPath(params.snpeff_cache).collect() : [[:], []] vep_cache = params.vep_cache ? Channel.fromPath(params.vep_cache).collect() : [] vep_extra_files = [] From 78fd7aef654ee3afb854cc58222892f4b975c93d Mon Sep 17 00:00:00 2001 From: asp8200 Date: Wed, 16 Aug 2023 07:59:18 +0000 Subject: [PATCH 10/21] Still trying to get call to SNPEFF working --- subworkflows/nf-core/vcf_annotate_snpeff/main.nf | 3 +-- workflows/sarek.nf | 4 ++-- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/subworkflows/nf-core/vcf_annotate_snpeff/main.nf b/subworkflows/nf-core/vcf_annotate_snpeff/main.nf index 2f37454d17..2a875939de 100644 --- a/subworkflows/nf-core/vcf_annotate_snpeff/main.nf +++ b/subworkflows/nf-core/vcf_annotate_snpeff/main.nf @@ -13,8 +13,7 @@ workflow VCF_ANNOTATE_SNPEFF { main: ch_versions = Channel.empty() - - SNPEFF_SNPEFF(ch_vcf, val_snpeff_db, ch_snpeff_cache.map{it -> [[:], it]}) + SNPEFF_SNPEFF(ch_vcf, val_snpeff_db, ch_snpeff_cache) TABIX_BGZIPTABIX(SNPEFF_SNPEFF.out.vcf) // Gather versions of all tools used diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 70a59ecaf3..2b59c8f0e0 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -312,8 +312,8 @@ vep_genome = params.vep_genome ?: Channel.empty() vep_species = params.vep_species ?: Channel.empty() // Initialize files channels based on params, not defined within the params.genomes[params.genome] scope -snpeff_cache = params.snpeff_cache ? Channel.fromPath(params.snpeff_cache).collect() : [[:], []] -vep_cache = params.vep_cache ? Channel.fromPath(params.vep_cache).collect() : [] +snpeff_cache = params.snpeff_cache ? Channel.fromPath(params.snpeff_cache).collect().map{it -> [[:], it]} : [[:], []] +vep_cache = params.vep_cache ? Channel.fromPath(params.vep_cache).collect() : [] vep_extra_files = [] From 26c4da9ab6b24043d53410894ea827fc3a70cf8a Mon Sep 17 00:00:00 2001 From: asp8200 Date: Wed, 16 Aug 2023 08:25:36 +0000 Subject: [PATCH 11/21] Fixing definition of snpeff_cache when downloading snpeff-cache --- workflows/sarek.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 2b59c8f0e0..dced8d1568 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -448,7 +448,7 @@ workflow SAREK { if (params.download_cache) { PREPARE_CACHE(ensemblvep_info, snpeff_info) - snpeff_cache = PREPARE_CACHE.out.snpeff_cache.map{ meta, cache -> [ cache ] } + snpeff_cache = PREPARE_CACHE.out.snpeff_cache vep_cache = PREPARE_CACHE.out.ensemblvep_cache.map{ meta, cache -> [ cache ] } versions = versions.mix(PREPARE_CACHE.out.versions) From 19e5beaeef513c5a4d6e127a667682d7ec8bb064 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Wed, 16 Aug 2023 09:00:42 +0000 Subject: [PATCH 12/21] Trying to revert controlfreec/makegraph to previous version. (Handling of ploidy in controlfreec will be part of upcoming release.) --- modules.json | 2 +- modules/nf-core/controlfreec/makegraph/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules.json b/modules.json index 158b9887c6..e69d2cca51 100644 --- a/modules.json +++ b/modules.json @@ -97,7 +97,7 @@ }, "controlfreec/makegraph": { "branch": "master", - "git_sha": "83ddd598664e16f74e0b5c728e9f81285c37e893", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf index 91231ad8c7..78068c8a77 100644 --- a/modules/nf-core/controlfreec/makegraph/main.nf +++ b/modules/nf-core/controlfreec/makegraph/main.nf @@ -8,7 +8,7 @@ process CONTROLFREEC_MAKEGRAPH { 'biocontainers/control-freec:11.6--h1b792b2_1' }" input: - tuple val(meta), path(ratio), path(baf), val(ploidy) + tuple val(meta), path(ratio), path(baf) output: tuple val(meta), path("*_BAF.png") , emit: png_baf From 922e019236837705c49dade0cd9e0c4518b91bcc Mon Sep 17 00:00:00 2001 From: asp8200 Date: Wed, 16 Aug 2023 10:07:56 +0000 Subject: [PATCH 13/21] Trying to revert controlfreec/makegraph to previous version. (2) --- modules/nf-core/controlfreec/makegraph/main.nf | 2 +- modules/nf-core/controlfreec/makegraph/meta.yml | 3 --- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf index 78068c8a77..293cf1feaa 100644 --- a/modules/nf-core/controlfreec/makegraph/main.nf +++ b/modules/nf-core/controlfreec/makegraph/main.nf @@ -25,7 +25,7 @@ process CONTROLFREEC_MAKEGRAPH { def prefix = task.ext.prefix ?: "${meta.id}" def baf = baf ?: "" """ - cat \$(which makeGraph.R) | R --slave --args ${ploidy} ${args} ${ratio} ${baf} + cat \$(which makeGraph.R) | R --slave --args ${args} ${ratio} ${baf} mv *_BAF.txt.png ${prefix}_BAF.png mv *_ratio.txt.log2.png ${prefix}_ratio.log2.png diff --git a/modules/nf-core/controlfreec/makegraph/meta.yml b/modules/nf-core/controlfreec/makegraph/meta.yml index 7b97dcf9bc..a207ec8c8f 100644 --- a/modules/nf-core/controlfreec/makegraph/meta.yml +++ b/modules/nf-core/controlfreec/makegraph/meta.yml @@ -30,9 +30,6 @@ input: type: file description: .BAF file generated by FREEC pattern: "*.BAF" - - ploidy: - type: integer - description: Ploidy value for which graph should be created output: - meta: From ce62d00762a48780c5c72d51fb004a570bb12f67 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Wed, 16 Aug 2023 11:13:34 +0000 Subject: [PATCH 14/21] Updating md5sums since cnvkit was updated. [skip ci] [skip actions] --- tests/test_cnvkit.yml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/tests/test_cnvkit.yml b/tests/test_cnvkit.yml index ef959455fc..3a1b8181cb 100644 --- a/tests/test_cnvkit.yml +++ b/tests/test_cnvkit.yml @@ -20,7 +20,7 @@ - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn md5sum: fe1248aa91fad7769303bb4c031d55ca - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.bintest.cns - md5sum: e55667a75d7d8eaec2efd3b611f15379 + md5sum: d8c43bead209cdf4c480284c64542693 - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.call.cns md5sum: 9968e02ef2f11ed22e2789c053f7159c - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.cnr @@ -46,13 +46,13 @@ - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn md5sum: 067115082c4af4b64d58c0dc3a3642e4 - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.bintest.cns - md5sum: e9a260b81a34d8bc75330435d2a5e8da + md5sum: 3950153843b43230c5d0fdf832740b5d - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.call.cns - md5sum: c7d7fd87b27e103f73988ae307450e82 + md5sum: ac3d073de1db84fa19077d8eda01b616 - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cnr - md5sum: 26c506866198d46610c71fa6c0f9e381 + md5sum: d7d437ae406ca2f00a6362277fe334ba - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cns - md5sum: 83510b274c24a2671a962477a1ceb436 + md5sum: d15bf5061d90c8edbcba04d2bd2a270c - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.targetcoverage.cnn md5sum: b4a49faf170e436ec32dcc21ccc3ce8f - path: results/cnvkit @@ -77,7 +77,7 @@ - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn md5sum: 067115082c4af4b64d58c0dc3a3642e4 - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.bintest.cns - md5sum: f6adc75a0a86b7a921eca1b79a394cb0 + md5sum: 7a66b5f63acb05e6dfb0784c215851ec - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.call.cns md5sum: f7caeca04aba28b125ce26b511f42afb - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.cnr @@ -110,7 +110,7 @@ - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn md5sum: fe1248aa91fad7769303bb4c031d55ca - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.bintest.cns - md5sum: e55667a75d7d8eaec2efd3b611f15379 + md5sum: d8c43bead209cdf4c480284c64542693 - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.call.cns md5sum: 9968e02ef2f11ed22e2789c053f7159c - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.cnr @@ -147,12 +147,12 @@ - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn md5sum: 067115082c4af4b64d58c0dc3a3642e4 - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.bintest.cns - md5sum: e9a260b81a34d8bc75330435d2a5e8da + md5sum: 3950153843b43230c5d0fdf832740b5d - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.call.cns - md5sum: c7d7fd87b27e103f73988ae307450e82 + md5sum: ac3d073de1db84fa19077d8eda01b616 - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cnr - md5sum: 26c506866198d46610c71fa6c0f9e381 + md5sum: d7d437ae406ca2f00a6362277fe334ba - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cns - md5sum: 83510b274c24a2671a962477a1ceb436 + md5sum: d15bf5061d90c8edbcba04d2bd2a270c - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.targetcoverage.cnn md5sum: b4a49faf170e436ec32dcc21ccc3ce8f From 944330bcd2f588479c5a1ca06e6bc25aefe547b1 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Wed, 16 Aug 2023 11:36:16 +0000 Subject: [PATCH 15/21] Replacing MSISENSORPRO_MSI_SOMATIC with SISENSORPRO_MSISOMATIC --- conf/modules/msisensorpro.config | 2 +- modules.json | 5 ++ .../nf-core/msisensorpro/msi_somatic/main.nf | 47 ------------------- .../bam_variant_calling_somatic_all/main.nf | 8 ++-- 4 files changed, 10 insertions(+), 52 deletions(-) delete mode 100644 modules/nf-core/msisensorpro/msi_somatic/main.nf diff --git a/conf/modules/msisensorpro.config b/conf/modules/msisensorpro.config index 574068e6b4..5c26afb8f4 100644 --- a/conf/modules/msisensorpro.config +++ b/conf/modules/msisensorpro.config @@ -15,7 +15,7 @@ process { - withName: 'MSISENSORPRO_MSI_SOMATIC' { + withName: 'MSISENSORPRO_MSISOMATIC' { publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/variant_calling/msisensorpro/${meta.id}/" }, diff --git a/modules.json b/modules.json index e69d2cca51..1df6c1857d 100644 --- a/modules.json +++ b/modules.json @@ -311,6 +311,11 @@ "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, + "msisensorpro/msisomatic": { + "branch": "master", + "git_sha": "5b5d7fba9e08624def34f40e3f4b9268f2eeabbc", + "installed_by": ["modules"] + }, "msisensorpro/scan": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", diff --git a/modules/nf-core/msisensorpro/msi_somatic/main.nf b/modules/nf-core/msisensorpro/msi_somatic/main.nf deleted file mode 100644 index 8e0189e4bb..0000000000 --- a/modules/nf-core/msisensorpro/msi_somatic/main.nf +++ /dev/null @@ -1,47 +0,0 @@ -process MSISENSORPRO_MSI_SOMATIC { - tag "$meta.id" - label 'process_low' - - conda "bioconda::msisensor-pro=1.2.0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : - 'biocontainers/msisensor-pro:1.2.0--hfc31af2_0' }" - - input: - tuple val(meta), path(normal), path(normal_index), path(tumor), path(tumor_index), path(intervals) - path (fasta) - path (msisensor_scan) - - output: - tuple val(meta), path("${prefix}") , emit: output_report - tuple val(meta), path("${prefix}_dis") , emit: output_dis - tuple val(meta), path("${prefix}_germline"), emit: output_germline - tuple val(meta), path("${prefix}_somatic") , emit: output_somatic - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" - def fasta = fasta ? "-g ${fasta}" : "" - def intervals = intervals ? " -e ${intervals} " : "" - """ - msisensor-pro \\ - msi \\ - -d ${msisensor_scan} \\ - -n ${normal} \\ - -t ${tumor} \\ - ${fasta} \\ - -o $prefix \\ - -b ${task.cpus} \\ - ${intervals} \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - msisensor-pro: \$(msisensor-pro 2>&1 | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p') - END_VERSIONS - """ -} diff --git a/subworkflows/local/bam_variant_calling_somatic_all/main.nf b/subworkflows/local/bam_variant_calling_somatic_all/main.nf index d407c70fc4..280c2277e5 100644 --- a/subworkflows/local/bam_variant_calling_somatic_all/main.nf +++ b/subworkflows/local/bam_variant_calling_somatic_all/main.nf @@ -12,7 +12,7 @@ include { BAM_VARIANT_CALLING_SOMATIC_MANTA } from '../bam_variant_c include { BAM_VARIANT_CALLING_SOMATIC_MUTECT2 } from '../bam_variant_calling_somatic_mutect2/main' include { BAM_VARIANT_CALLING_SOMATIC_STRELKA } from '../bam_variant_calling_somatic_strelka/main' include { BAM_VARIANT_CALLING_SOMATIC_TIDDIT } from '../bam_variant_calling_somatic_tiddit/main' -include { MSISENSORPRO_MSI_SOMATIC } from '../../../modules/nf-core/msisensorpro/msi_somatic/main' +include { MSISENSORPRO_MSISOMATIC } from '../../../modules/nf-core/msisensorpro/msisomatic/main' workflow BAM_VARIANT_CALLING_SOMATIC_ALL { take: @@ -173,10 +173,10 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL { // MSISENSOR if (tools.split(',').contains('msisensorpro')) { - MSISENSORPRO_MSI_SOMATIC(cram.combine(intervals_bed_combined), fasta, msisensorpro_scan) + MSISENSORPRO_MSISOMATIC(cram.combine(intervals_bed_combined), fasta, msisensorpro_scan) - versions = versions.mix(MSISENSORPRO_MSI_SOMATIC.out.versions) - out_msisensorpro = out_msisensorpro.mix(MSISENSORPRO_MSI_SOMATIC.out.output_report) + versions = versions.mix(MSISENSORPRO_MSISOMATIC.out.versions) + out_msisensorpro = out_msisensorpro.mix(MSISENSORPRO_MSISOMATIC.out.output_report) } // MUTECT2 From a07f1a806c1aa87da7562eda0a36a3ea197f716c Mon Sep 17 00:00:00 2001 From: asp8200 Date: Wed, 16 Aug 2023 11:50:58 +0000 Subject: [PATCH 16/21] Replacing MSISENSORPRO_MSI_SOMATIC with SISENSORPRO_MSISOMATIC. (2) --- .../nf-core/msisensorpro/msisomatic/main.nf | 47 +++++++++++++++++++ .../{msi_somatic => msisomatic}/meta.yml | 2 +- 2 files changed, 48 insertions(+), 1 deletion(-) create mode 100644 modules/nf-core/msisensorpro/msisomatic/main.nf rename modules/nf-core/msisensorpro/{msi_somatic => msisomatic}/meta.yml (98%) diff --git a/modules/nf-core/msisensorpro/msisomatic/main.nf b/modules/nf-core/msisensorpro/msisomatic/main.nf new file mode 100644 index 0000000000..50287cb3cd --- /dev/null +++ b/modules/nf-core/msisensorpro/msisomatic/main.nf @@ -0,0 +1,47 @@ +process MSISENSORPRO_MSISOMATIC { + tag "$meta.id" + label 'process_low' + + conda "bioconda::msisensor-pro=1.2.0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : + 'biocontainers/msisensor-pro:1.2.0--hfc31af2_0' }" + + input: + tuple val(meta), path(normal), path(normal_index), path(tumor), path(tumor_index), path(intervals) + path (fasta) + path (msisensor_scan) + + output: + tuple val(meta), path("${prefix}") , emit: output_report + tuple val(meta), path("${prefix}_dis") , emit: output_dis + tuple val(meta), path("${prefix}_germline"), emit: output_germline + tuple val(meta), path("${prefix}_somatic") , emit: output_somatic + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def fasta = fasta ? "-g ${fasta}" : "" + def intervals = intervals ? " -e ${intervals} " : "" + """ + msisensor-pro \\ + msi \\ + -d ${msisensor_scan} \\ + -n ${normal} \\ + -t ${tumor} \\ + ${fasta} \\ + -o $prefix \\ + -b ${task.cpus} \\ + ${intervals} \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + msisensor-pro: \$(msisensor-pro 2>&1 | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p') + END_VERSIONS + """ +} diff --git a/modules/nf-core/msisensorpro/msi_somatic/meta.yml b/modules/nf-core/msisensorpro/msisomatic/meta.yml similarity index 98% rename from modules/nf-core/msisensorpro/msi_somatic/meta.yml rename to modules/nf-core/msisensorpro/msisomatic/meta.yml index 480f67271e..bcd95dc72b 100644 --- a/modules/nf-core/msisensorpro/msi_somatic/meta.yml +++ b/modules/nf-core/msisensorpro/msisomatic/meta.yml @@ -1,4 +1,4 @@ -name: msisensorpro_msi_somatic +name: msisensorpro_msisomatic description: MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input keywords: - micro-satellite-scan From a124548315d855bec9d189574296fdbc02ba9705 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Wed, 16 Aug 2023 13:13:27 +0000 Subject: [PATCH 17/21] Updating changelog --- CHANGELOG.md | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4c310d080a..f23990b949 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1166](https://github.com/nf-core/sarek/pull/1166) - More info about `--tools` - [#1174](https://github.com/nf-core/sarek/pull/1174) - Updating multiqc to v1.15 - [#1179](https://github.com/nf-core/sarek/pull/1179) - Unhide params `trim_fastq`, `umi_read_structure`, and `aligner` +- [#1180](https://github.com/nf-core/sarek/pull/1180) - Updating the nf-core modules used by Sarek ### Fixed @@ -38,10 +39,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Dependencies -| Dependency | Old version | New version | -| ---------- | ----------- | ----------- | -| `multiqc` | 1.14 | 1.15 | -| `tiddit` | 3.3.2 | 3.6.1 | +| Dependency | Old version | New version | +| ------------------------ | ------------------------- | ------------------------ | +| `cnvkit` | 0.9.9 (`samtools` 1.16.1) | 0.9.10 (`samtools` 1.17) | +| `ensembl-vep` | 108 | 110 | +| `grep` (in untar-module) | 3.4 | 3.11 | +| `multiqc` | 1.14 | 1.15 | +| `tiddit` | 3.3.2 | 3.6.1 | ## [3.2.3](https://github.com/nf-core/sarek/releases/tag/3.2.3) - Gällivare From be28b635ea5fd685caa1a7e96103ebff48c395e3 Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Date: Thu, 17 Aug 2023 10:06:20 +0200 Subject: [PATCH 18/21] Update modules.json Co-authored-by: Friederike Hanssen --- modules.json | 5 ----- 1 file changed, 5 deletions(-) diff --git a/modules.json b/modules.json index 1df6c1857d..8ee0465542 100644 --- a/modules.json +++ b/modules.json @@ -306,11 +306,6 @@ "git_sha": "ebb27711cd5f4de921244bfa81c676504072d31c", "installed_by": ["modules"] }, - "msisensorpro/msi_somatic": { - "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": ["modules"] - }, "msisensorpro/msisomatic": { "branch": "master", "git_sha": "5b5d7fba9e08624def34f40e3f4b9268f2eeabbc", From bd8d39df5e225acf228de27442871b1452c3af96 Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Date: Thu, 17 Aug 2023 10:06:52 +0200 Subject: [PATCH 19/21] Update CHANGELOG.md Co-authored-by: Friederike Hanssen --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f23990b949..c089ad282f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -43,7 +43,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | ------------------------ | ------------------------- | ------------------------ | | `cnvkit` | 0.9.9 (`samtools` 1.16.1) | 0.9.10 (`samtools` 1.17) | | `ensembl-vep` | 108 | 110 | -| `grep` (in untar-module) | 3.4 | 3.11 | +| `grep` | 3.4 | 3.11 | | `multiqc` | 1.14 | 1.15 | | `tiddit` | 3.3.2 | 3.6.1 | From 766b61e3a0aca1f322cf855159fa049c4a9a7d15 Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Date: Thu, 17 Aug 2023 10:07:03 +0200 Subject: [PATCH 20/21] Update CHANGELOG.md Co-authored-by: Friederike Hanssen --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c089ad282f..3d061abb82 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,7 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1166](https://github.com/nf-core/sarek/pull/1166) - More info about `--tools` - [#1174](https://github.com/nf-core/sarek/pull/1174) - Updating multiqc to v1.15 - [#1179](https://github.com/nf-core/sarek/pull/1179) - Unhide params `trim_fastq`, `umi_read_structure`, and `aligner` -- [#1180](https://github.com/nf-core/sarek/pull/1180) - Updating the nf-core modules used by Sarek +- [#1180](https://github.com/nf-core/sarek/pull/1180) - Updating the nf-core modules ### Fixed From 3b4e8bd84144b67fedb11247fb9e7124e519cc44 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 17 Aug 2023 08:35:03 +0000 Subject: [PATCH 21/21] [automated] Fix linting with Prettier --- CHANGELOG.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3d061abb82..cb82576660 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -39,13 +39,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Dependencies -| Dependency | Old version | New version | -| ------------------------ | ------------------------- | ------------------------ | -| `cnvkit` | 0.9.9 (`samtools` 1.16.1) | 0.9.10 (`samtools` 1.17) | -| `ensembl-vep` | 108 | 110 | -| `grep` | 3.4 | 3.11 | -| `multiqc` | 1.14 | 1.15 | -| `tiddit` | 3.3.2 | 3.6.1 | +| Dependency | Old version | New version | +| ------------- | ------------------------- | ------------------------ | +| `cnvkit` | 0.9.9 (`samtools` 1.16.1) | 0.9.10 (`samtools` 1.17) | +| `ensembl-vep` | 108 | 110 | +| `grep` | 3.4 | 3.11 | +| `multiqc` | 1.14 | 1.15 | +| `tiddit` | 3.3.2 | 3.6.1 | ## [3.2.3](https://github.com/nf-core/sarek/releases/tag/3.2.3) - Gällivare