diff --git a/CHANGELOG.md b/CHANGELOG.md index 4c310d080a..cb82576660 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 ### 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` | 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 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 fb43a04071..8ee0465542 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": { @@ -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": { @@ -303,12 +303,12 @@ }, "mosdepth": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "ebb27711cd5f4de921244bfa81c676504072d31c", "installed_by": ["modules"] }, - "msisensorpro/msi_somatic": { + "msisensorpro/msisomatic": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "5b5d7fba9e08624def34f40e3f4b9268f2eeabbc", "installed_by": ["modules"] }, "msisensorpro/scan": { @@ -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/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 ${bed}" : "" if (bed && args.contains("--by")) { - exit 1, "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition" + error "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition" } if (!bed && args.contains("--thresholds")) { - exit 1, "'--thresholds' can only be specified in conjunction with '--by'" + error "'--thresholds' can only be specified in conjunction with '--by'" } """ diff --git a/modules/nf-core/msisensorpro/msi_somatic/main.nf b/modules/nf-core/msisensorpro/msisomatic/main.nf similarity index 97% rename from modules/nf-core/msisensorpro/msi_somatic/main.nf rename to modules/nf-core/msisensorpro/msisomatic/main.nf index 8e0189e4bb..50287cb3cd 100644 --- a/modules/nf-core/msisensorpro/msi_somatic/main.nf +++ b/modules/nf-core/msisensorpro/msisomatic/main.nf @@ -1,4 +1,4 @@ -process MSISENSORPRO_MSI_SOMATIC { +process MSISENSORPRO_MSISOMATIC { tag "$meta.id" label 'process_low' 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 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/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) 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 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..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 diff --git a/subworkflows/local/vcf_qc_bcftools_vcftools/main.nf b/subworkflows/local/vcf_qc_bcftools_vcftools/main.nf index 55fbf59bd9..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, []) 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/main.nf b/subworkflows/nf-core/vcf_annotate_snpeff/main.nf index 3570a5b7c0..2a875939de 100644 --- a/subworkflows/nf-core/vcf_annotate_snpeff/main.nf +++ b/subworkflows/nf-core/vcf_annotate_snpeff/main.nf @@ -13,7 +13,6 @@ workflow VCF_ANNOTATE_SNPEFF { main: ch_versions = Channel.empty() - SNPEFF_SNPEFF(ch_vcf, val_snpeff_db, ch_snpeff_cache) TABIX_BGZIPTABIX(SNPEFF_SNPEFF.out.vcf) 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: 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 diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 669dac1bd5..dced8d1568 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 = [] @@ -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)