From 967fb22dedc2c8855f00e64c3d7b5814c85242a6 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Tue, 15 Feb 2022 11:29:36 +0100 Subject: [PATCH] Update versions (#1292) * Update versions * update checksums + remove variables as input for applyvqsr * sneak in removal of values and provide them via modules.config * update another checksum * more checksums * move vairable to config * remove controlfreec, wrong branch * add line break --- modules/gatk4/applybqsr/main.nf | 6 +++--- modules/gatk4/applyvqsr/main.nf | 15 +++----------- modules/gatk4/applyvqsr/meta.yml | 12 ----------- modules/gatk4/baserecalibrator/main.nf | 6 +++--- modules/gatk4/bedtointervallist/main.nf | 6 +++--- modules/gatk4/calculatecontamination/main.nf | 6 +++--- .../gatk4/createsequencedictionary/main.nf | 6 +++--- .../gatk4/createsomaticpanelofnormals/main.nf | 6 +++--- .../gatk4/estimatelibrarycomplexity/main.nf | 6 +++--- modules/gatk4/fastqtosam/main.nf | 6 +++--- modules/gatk4/filtermutectcalls/main.nf | 6 +++--- modules/gatk4/gatherbqsrreports/main.nf | 6 +++--- modules/gatk4/genomicsdbimport/main.nf | 6 +++--- modules/gatk4/genotypegvcfs/main.nf | 6 +++--- modules/gatk4/getpileupsummaries/main.nf | 6 +++--- modules/gatk4/haplotypecaller/main.nf | 6 +++--- modules/gatk4/indexfeaturefile/main.nf | 6 +++--- modules/gatk4/intervallisttools/main.nf | 6 +++--- .../gatk4/learnreadorientationmodel/main.nf | 6 +++--- modules/gatk4/markduplicates/main.nf | 6 +++--- modules/gatk4/mergebamalignment/main.nf | 6 +++--- modules/gatk4/mergevcfs/main.nf | 6 +++--- modules/gatk4/mutect2/main.nf | 6 +++--- modules/gatk4/revertsam/main.nf | 6 +++--- modules/gatk4/samtofastq/main.nf | 6 +++--- modules/gatk4/splitncigarreads/main.nf | 6 +++--- modules/gatk4/variantfiltration/main.nf | 6 +++--- modules/gatk4/variantrecalibrator/main.nf | 20 ++++--------------- modules/gatk4/variantrecalibrator/meta.yml | 20 ------------------- tests/modules/gatk4/applybqsr/test.yml | 12 +++++------ tests/modules/gatk4/applyvqsr/main.nf | 13 ++++-------- tests/modules/gatk4/applyvqsr/nextflow.config | 8 +++++++- tests/modules/gatk4/applyvqsr/test.yml | 4 ++-- .../gatk4/calculatecontamination/test.yml | 6 +++--- tests/modules/gatk4/fastqtosam/test.yml | 4 ++-- .../modules/gatk4/gatherbqsrreports/test.yml | 4 ++-- tests/modules/gatk4/genomicsdbimport/test.yml | 6 +++--- .../modules/gatk4/getpileupsummaries/test.yml | 6 +++--- tests/modules/gatk4/indexfeaturefile/test.yml | 6 +++--- tests/modules/gatk4/markduplicates/test.yml | 12 +++++------ tests/modules/gatk4/splitncigarreads/test.yml | 4 ++-- .../modules/gatk4/variantrecalibrator/main.nf | 15 ++++---------- .../gatk4/variantrecalibrator/nextflow.config | 8 +++++++- 43 files changed, 136 insertions(+), 189 deletions(-) diff --git a/modules/gatk4/applybqsr/main.nf b/modules/gatk4/applybqsr/main.nf index 672e93e0..851afc04 100644 --- a/modules/gatk4/applybqsr/main.nf +++ b/modules/gatk4/applybqsr/main.nf @@ -2,10 +2,10 @@ process GATK4_APPLYBQSR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/gatk4/applyvqsr/main.nf b/modules/gatk4/applyvqsr/main.nf index 006840b3..3049aa79 100644 --- a/modules/gatk4/applyvqsr/main.nf +++ b/modules/gatk4/applyvqsr/main.nf @@ -2,19 +2,16 @@ process GATK4_APPLYVQSR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi), path(recal), path(recalidx), path(tranches) path fasta path fai path dict - val allelespecific - val truthsensitivity - val mode output: tuple val(meta), path("*.vcf.gz") , emit: vcf @@ -28,9 +25,6 @@ process GATK4_APPLYVQSR { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" refCommand = fasta ? "-R ${fasta} " : '' - alleleSpecificCommand = allelespecific ? '-AS' : '' - truthSensitivityCommand = truthsensitivity ? "--truth-sensitivity-filter-level ${truthsensitivity}" : '' - modeCommand = mode ? "--mode ${mode} " : 'SNP' def avail_mem = 3 if (!task.memory) { @@ -43,11 +37,8 @@ process GATK4_APPLYVQSR { ${refCommand} \\ -V ${vcf} \\ -O ${prefix}.vcf.gz \\ - ${alleleSpecificCommand} \\ - ${truthSensitivityCommand} \\ --tranches-file $tranches \\ --recal-file $recal \\ - ${modeCommand} \\ $args cat <<-END_VERSIONS > versions.yml diff --git a/modules/gatk4/applyvqsr/meta.yml b/modules/gatk4/applyvqsr/meta.yml index b757f3e9..746d22ac 100644 --- a/modules/gatk4/applyvqsr/meta.yml +++ b/modules/gatk4/applyvqsr/meta.yml @@ -57,18 +57,6 @@ input: type: file description: GATK sequence dictionary pattern: "*.dict" - - allelespecific: - type: boolean - description: Whether or not to run ApplyVQSR in allele specific mode, this should be kept the same as the stage 1 VariantRecalibrator run. - pattern: "{true,false}" - - truthsensitivity: - type: double - description: Value to be used as the truth sensitivity cutoff score. - pattern: "99.0" - - mode: - type: String - description: Specifies which recalibration mode to employ, should be the same as the stage 1 VariantRecalibrator run. (SNP is default, BOTH is intended for testing only) - pattern: "{SNP,INDEL,BOTH}" output: - vcf: diff --git a/modules/gatk4/baserecalibrator/main.nf b/modules/gatk4/baserecalibrator/main.nf index 48c127f0..ecb41d9b 100644 --- a/modules/gatk4/baserecalibrator/main.nf +++ b/modules/gatk4/baserecalibrator/main.nf @@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/gatk4/bedtointervallist/main.nf b/modules/gatk4/bedtointervallist/main.nf index 9f2b2dfe..74256dd1 100644 --- a/modules/gatk4/bedtointervallist/main.nf +++ b/modules/gatk4/bedtointervallist/main.nf @@ -2,10 +2,10 @@ process GATK4_BEDTOINTERVALLIST { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(bed) diff --git a/modules/gatk4/calculatecontamination/main.nf b/modules/gatk4/calculatecontamination/main.nf index 177f4878..298739ab 100644 --- a/modules/gatk4/calculatecontamination/main.nf +++ b/modules/gatk4/calculatecontamination/main.nf @@ -2,10 +2,10 @@ process GATK4_CALCULATECONTAMINATION { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(pileup), path(matched) diff --git a/modules/gatk4/createsequencedictionary/main.nf b/modules/gatk4/createsequencedictionary/main.nf index 714843c2..87d52a59 100644 --- a/modules/gatk4/createsequencedictionary/main.nf +++ b/modules/gatk4/createsequencedictionary/main.nf @@ -2,10 +2,10 @@ process GATK4_CREATESEQUENCEDICTIONARY { tag "$fasta" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: path fasta diff --git a/modules/gatk4/createsomaticpanelofnormals/main.nf b/modules/gatk4/createsomaticpanelofnormals/main.nf index a82c24d8..c030f4e3 100644 --- a/modules/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/gatk4/createsomaticpanelofnormals/main.nf @@ -2,10 +2,10 @@ process GATK4_CREATESOMATICPANELOFNORMALS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(genomicsdb) diff --git a/modules/gatk4/estimatelibrarycomplexity/main.nf b/modules/gatk4/estimatelibrarycomplexity/main.nf index 2894e305..ba68bf70 100644 --- a/modules/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/gatk4/estimatelibrarycomplexity/main.nf @@ -2,10 +2,10 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(cram) diff --git a/modules/gatk4/fastqtosam/main.nf b/modules/gatk4/fastqtosam/main.nf index 631c0394..0c85a74f 100644 --- a/modules/gatk4/fastqtosam/main.nf +++ b/modules/gatk4/fastqtosam/main.nf @@ -2,10 +2,10 @@ process GATK4_FASTQTOSAM { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/gatk4/filtermutectcalls/main.nf b/modules/gatk4/filtermutectcalls/main.nf index a7dd9a61..77175c7d 100644 --- a/modules/gatk4/filtermutectcalls/main.nf +++ b/modules/gatk4/filtermutectcalls/main.nf @@ -2,10 +2,10 @@ process GATK4_FILTERMUTECTCALLS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi), path(stats), path(orientationbias), path(segmentation), path(contaminationfile), val(contaminationest) diff --git a/modules/gatk4/gatherbqsrreports/main.nf b/modules/gatk4/gatherbqsrreports/main.nf index f8d91a92..279f1ac8 100644 --- a/modules/gatk4/gatherbqsrreports/main.nf +++ b/modules/gatk4/gatherbqsrreports/main.nf @@ -2,10 +2,10 @@ process GATK4_GATHERBQSRREPORTS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(recal_table) diff --git a/modules/gatk4/genomicsdbimport/main.nf b/modules/gatk4/genomicsdbimport/main.nf index e88471e1..d2d89ccc 100644 --- a/modules/gatk4/genomicsdbimport/main.nf +++ b/modules/gatk4/genomicsdbimport/main.nf @@ -2,10 +2,10 @@ process GATK4_GENOMICSDBIMPORT { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi), path(intervalfile), val(intervalval), path(wspace) diff --git a/modules/gatk4/genotypegvcfs/main.nf b/modules/gatk4/genotypegvcfs/main.nf index c3e41229..2b0982de 100644 --- a/modules/gatk4/genotypegvcfs/main.nf +++ b/modules/gatk4/genotypegvcfs/main.nf @@ -2,10 +2,10 @@ process GATK4_GENOTYPEGVCFS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(gvcf), path(gvcf_index), path(intervals) diff --git a/modules/gatk4/getpileupsummaries/main.nf b/modules/gatk4/getpileupsummaries/main.nf index 6d98874f..5395c068 100644 --- a/modules/gatk4/getpileupsummaries/main.nf +++ b/modules/gatk4/getpileupsummaries/main.nf @@ -2,10 +2,10 @@ process GATK4_GETPILEUPSUMMARIES { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(index), path(intervals) diff --git a/modules/gatk4/haplotypecaller/main.nf b/modules/gatk4/haplotypecaller/main.nf index 6f03ffd2..33871fcf 100644 --- a/modules/gatk4/haplotypecaller/main.nf +++ b/modules/gatk4/haplotypecaller/main.nf @@ -2,10 +2,10 @@ process GATK4_HAPLOTYPECALLER { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/gatk4/indexfeaturefile/main.nf b/modules/gatk4/indexfeaturefile/main.nf index b5add0e0..275e51f5 100644 --- a/modules/gatk4/indexfeaturefile/main.nf +++ b/modules/gatk4/indexfeaturefile/main.nf @@ -2,10 +2,10 @@ process GATK4_INDEXFEATUREFILE { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(feature_file) diff --git a/modules/gatk4/intervallisttools/main.nf b/modules/gatk4/intervallisttools/main.nf index 40c7fb19..352a3240 100644 --- a/modules/gatk4/intervallisttools/main.nf +++ b/modules/gatk4/intervallisttools/main.nf @@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOOLS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(interval_list) diff --git a/modules/gatk4/learnreadorientationmodel/main.nf b/modules/gatk4/learnreadorientationmodel/main.nf index 7d96c27e..4771a158 100644 --- a/modules/gatk4/learnreadorientationmodel/main.nf +++ b/modules/gatk4/learnreadorientationmodel/main.nf @@ -2,10 +2,10 @@ process GATK4_LEARNREADORIENTATIONMODEL { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(f1r2) diff --git a/modules/gatk4/markduplicates/main.nf b/modules/gatk4/markduplicates/main.nf index 735b093e..6b150655 100644 --- a/modules/gatk4/markduplicates/main.nf +++ b/modules/gatk4/markduplicates/main.nf @@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(bams) diff --git a/modules/gatk4/mergebamalignment/main.nf b/modules/gatk4/mergebamalignment/main.nf index e636e1cd..cfeb23dd 100644 --- a/modules/gatk4/mergebamalignment/main.nf +++ b/modules/gatk4/mergebamalignment/main.nf @@ -2,10 +2,10 @@ process GATK4_MERGEBAMALIGNMENT { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(aligned), path(unmapped) diff --git a/modules/gatk4/mergevcfs/main.nf b/modules/gatk4/mergevcfs/main.nf index 3e9973e7..54e38667 100644 --- a/modules/gatk4/mergevcfs/main.nf +++ b/modules/gatk4/mergevcfs/main.nf @@ -2,10 +2,10 @@ process GATK4_MERGEVCFS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(vcfs) diff --git a/modules/gatk4/mutect2/main.nf b/modules/gatk4/mutect2/main.nf index a7afe86d..568d3393 100644 --- a/modules/gatk4/mutect2/main.nf +++ b/modules/gatk4/mutect2/main.nf @@ -2,10 +2,10 @@ process GATK4_MUTECT2 { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta) , path(input) , path(input_index) , path(intervals), val(which_norm) diff --git a/modules/gatk4/revertsam/main.nf b/modules/gatk4/revertsam/main.nf index 23f99ab4..b3bf9f95 100644 --- a/modules/gatk4/revertsam/main.nf +++ b/modules/gatk4/revertsam/main.nf @@ -2,10 +2,10 @@ process GATK4_REVERTSAM { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/gatk4/samtofastq/main.nf b/modules/gatk4/samtofastq/main.nf index 2da40b6c..53e5013f 100644 --- a/modules/gatk4/samtofastq/main.nf +++ b/modules/gatk4/samtofastq/main.nf @@ -2,10 +2,10 @@ process GATK4_SAMTOFASTQ { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/gatk4/splitncigarreads/main.nf b/modules/gatk4/splitncigarreads/main.nf index 6d0a35fd..fdd1d974 100644 --- a/modules/gatk4/splitncigarreads/main.nf +++ b/modules/gatk4/splitncigarreads/main.nf @@ -2,10 +2,10 @@ process GATK4_SPLITNCIGARREADS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/gatk4/variantfiltration/main.nf b/modules/gatk4/variantfiltration/main.nf index 3a41d20c..68f3d636 100644 --- a/modules/gatk4/variantfiltration/main.nf +++ b/modules/gatk4/variantfiltration/main.nf @@ -2,10 +2,10 @@ process GATK4_VARIANTFILTRATION { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(vcf), path(vcf_tbi) diff --git a/modules/gatk4/variantrecalibrator/main.nf b/modules/gatk4/variantrecalibrator/main.nf index df8a9599..31c9efbd 100644 --- a/modules/gatk4/variantrecalibrator/main.nf +++ b/modules/gatk4/variantrecalibrator/main.nf @@ -2,21 +2,17 @@ process GATK4_VARIANTRECALIBRATOR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(vcf) , path(tbi) path fasta path fai path dict - val allelespecific tuple path(resvcfs), path(restbis), val(reslabels) - val annotation - val mode - val create_rscript output: tuple val(meta), path("*.recal") , emit: recal @@ -32,11 +28,7 @@ process GATK4_VARIANTRECALIBRATOR { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" refCommand = fasta ? "-R ${fasta} " : '' - alleleSpecificCommand = allelespecific ? '-AS' : '' resourceCommand = '--resource:' + reslabels.join( ' --resource:') - annotationCommand = '-an ' + annotation.join( ' -an ') - modeCommand = mode ? "--mode ${mode} " : 'SNP' - rscriptCommand = create_rscript ? "--rscript-file ${prefix}.plots.R" : '' def avail_mem = 3 if (!task.memory) { @@ -48,13 +40,9 @@ process GATK4_VARIANTRECALIBRATOR { gatk --java-options "-Xmx${avail_mem}g" VariantRecalibrator \\ ${refCommand} \\ -V ${vcf} \\ - ${alleleSpecificCommand} \\ - ${resourceCommand} \\ - ${annotationCommand} \\ - ${modeCommand} \\ -O ${prefix}.recal \\ --tranches-file ${prefix}.tranches \\ - ${rscriptCommand}\\ + ${resourceCommand} \\ $args cat <<-END_VERSIONS > versions.yml diff --git a/modules/gatk4/variantrecalibrator/meta.yml b/modules/gatk4/variantrecalibrator/meta.yml index 92416a58..aac44b3a 100644 --- a/modules/gatk4/variantrecalibrator/meta.yml +++ b/modules/gatk4/variantrecalibrator/meta.yml @@ -45,10 +45,6 @@ input: type: file description: GATK sequence dictionary pattern: "*.dict" - - allelespecific: - type: boolean - description: specify whether to use allele specific annotations - pattern: "{true,false}" - resvcfs: type: list description: resource files to be used as truth, training and known sites resources, this imports the files into the module, file names are specified again in the resource_labels to be called via the command. @@ -57,22 +53,6 @@ input: type: list description: tbis for the corresponding vcfs files to be used as truth, training and known resources. pattern: '*/hapmap_3.3.hg38_chr21.vcf.gz.tbi' - - reslabels: - type: list - description: labels for the resource files to be used as truth, training and known sites resources, label should include an identifier,which kind of resource(s) it is, prior value and name of the file. - pattern: "hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38_chr21.vcf.gz" - - annotation: - type: list - description: specify which annotations should be used for calculations. - pattern: "['QD', 'MQ', 'FS', 'SOR']" - - mode: - type: string - description: specifies which recalibration mode to employ (SNP is default, BOTH is intended for testing only) - pattern: "{SNP,INDEL,BOTH}" - - rscript: - type: boolean - description: specify whether to generate rscript.plot output file - pattern: "{true,false}" output: - recal: type: file diff --git a/tests/modules/gatk4/applybqsr/test.yml b/tests/modules/gatk4/applybqsr/test.yml index 7449c210..4520c34b 100644 --- a/tests/modules/gatk4/applybqsr/test.yml +++ b/tests/modules/gatk4/applybqsr/test.yml @@ -5,9 +5,9 @@ - gatk4/applybqsr files: - path: output/gatk4/test.bam - md5sum: 908825edf1f229a072f91d8b753d95dd + md5sum: d088422be886dc8507ff97fcc7dd968a - path: output/gatk4/versions.yml - md5sum: b65c46529ae9658db0c596cbc26505c2 + md5sum: d5c6455d8a77aecc63f87c795fc3443e - name: gatk4 applybqsr test_gatk4_applybqsr_intervals command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config @@ -16,9 +16,9 @@ - gatk4/applybqsr files: - path: output/gatk4/test.bam - md5sum: 50f8a79c7d528e02470416f81eb582bc + md5sum: 4bfa18d651abd945e240b05e70107716 - path: output/gatk4/versions.yml - md5sum: 17c8a40b3537e3400edebd1826d28385 + md5sum: cb4cb8a62e117b4adc643ae47883d53c - name: gatk4 applybqsr test_gatk4_applybqsr_cram command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_cram -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config @@ -27,6 +27,6 @@ - gatk4/applybqsr files: - path: output/gatk4/test.cram - md5sum: cd8d4ba6181f714e74641adeb2f9aa1d + md5sum: 2e0bca197af4f043a4a85152e6edbe04 - path: output/gatk4/versions.yml - md5sum: 35218922e1929c699ea64de9f4c29fb5 + md5sum: 1efaa18be943bab4e4c54191d6eaa260 diff --git a/tests/modules/gatk4/applyvqsr/main.nf b/tests/modules/gatk4/applyvqsr/main.nf index 90a57aaa..c6e99d5c 100644 --- a/tests/modules/gatk4/applyvqsr/main.nf +++ b/tests/modules/gatk4/applyvqsr/main.nf @@ -2,7 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK4_APPLYVQSR } from '../../../../modules/gatk4/applyvqsr/main.nf' +include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_NO_ALLELSPECIFICITY } from '../../../../modules/gatk4/applyvqsr/main.nf' +include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY} from '../../../../modules/gatk4/applyvqsr/main.nf' workflow test_gatk4_applyvqsr { input = [ [ id:'test'], // meta map @@ -15,11 +16,8 @@ workflow test_gatk4_applyvqsr { fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) - allelespecific = false - truthsensitivity = '99.0' - mode = 'SNP' - GATK4_APPLYVQSR ( input, fasta, fai, dict, allelespecific, truthsensitivity, mode ) + GATK4_APPLYVQSR_NO_ALLELSPECIFICITY ( input, fasta, fai, dict ) } workflow test_gatk4_applyvqsr_allele_specific { @@ -33,9 +31,6 @@ workflow test_gatk4_applyvqsr_allele_specific { fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) - allelespecific = true - truthsensitivity = '99.0' - mode = 'SNP' - GATK4_APPLYVQSR ( input, fasta, fai, dict, allelespecific, truthsensitivity, mode ) + GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY ( input, fasta, fai, dict) } diff --git a/tests/modules/gatk4/applyvqsr/nextflow.config b/tests/modules/gatk4/applyvqsr/nextflow.config index 19934e76..bf943c23 100644 --- a/tests/modules/gatk4/applyvqsr/nextflow.config +++ b/tests/modules/gatk4/applyvqsr/nextflow.config @@ -1,5 +1,11 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + withName: GATK4_APPLYVQSR_NO_ALLELSPECIFICITY { + ext.args = '--mode SNP --truth-sensitivity-filter-level 99.0' + } -} \ No newline at end of file + withName: GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY { + ext.args = '--mode SNP --truth-sensitivity-filter-level 99.0 -AS' + } +} diff --git a/tests/modules/gatk4/applyvqsr/test.yml b/tests/modules/gatk4/applyvqsr/test.yml index b2acc6d8..7cb91c43 100644 --- a/tests/modules/gatk4/applyvqsr/test.yml +++ b/tests/modules/gatk4/applyvqsr/test.yml @@ -7,7 +7,7 @@ - path: output/gatk4/test.vcf.gz - path: output/gatk4/test.vcf.gz.tbi - path: output/gatk4/versions.yml - md5sum: 524a78cdfa56c8b09a4ff3f4cb278261 + md5sum: ce9c443375683e7f2958fe958759ad29 - name: gatk4 applyvqsr test_gatk4_applyvqsr_allele_specific command: nextflow run tests/modules/gatk4/applyvqsr -entry test_gatk4_applyvqsr_allele_specific -c tests/config/nextflow.config -c ./tests/modules/gatk4/applyvqsr/nextflow.config @@ -18,4 +18,4 @@ - path: output/gatk4/test.vcf.gz - path: output/gatk4/test.vcf.gz.tbi - path: output/gatk4/versions.yml - md5sum: 7a3c6e97628bd1f5f4e7fd429bf74a8e + md5sum: 521353d12d576de2864f1d18a3e54f14 diff --git a/tests/modules/gatk4/calculatecontamination/test.yml b/tests/modules/gatk4/calculatecontamination/test.yml index d598d1c0..4b73851d 100644 --- a/tests/modules/gatk4/calculatecontamination/test.yml +++ b/tests/modules/gatk4/calculatecontamination/test.yml @@ -7,7 +7,7 @@ - path: output/gatk4/test.contamination.table md5sum: 46c708c943b453da89a3da08acfdb2a7 - path: output/gatk4/versions.yml - md5sum: 79575dc2e6a7f0361f2d8b090c496070 + md5sum: 3da8f1c0de968886330a3f7a3a1c6616 - name: gatk4 calculatecontamination test_gatk4_calculatecontamination_matched_pair command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_matched_pair -c tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config @@ -18,7 +18,7 @@ - path: output/gatk4/test.contamination.table md5sum: 46c708c943b453da89a3da08acfdb2a7 - path: output/gatk4/versions.yml - md5sum: 733f15ef7eb504daec9fd8cd9beef71a + md5sum: 14ab12a71b0c2b87d8cd53639a991b3a - name: gatk4 calculatecontamination test_gatk4_calculatecontamination_segmentation command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_segmentation -c tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config @@ -31,4 +31,4 @@ - path: output/gatk4/test.segmentation.table md5sum: f4643d9319bde4efbfbe516d6fb13052 - path: output/gatk4/versions.yml - md5sum: 5396e33146addbe4a59d0f30cb573a3a + md5sum: d2e61315de31f512e448f0cb4b77db54 diff --git a/tests/modules/gatk4/fastqtosam/test.yml b/tests/modules/gatk4/fastqtosam/test.yml index 7f6357e8..07f9af15 100644 --- a/tests/modules/gatk4/fastqtosam/test.yml +++ b/tests/modules/gatk4/fastqtosam/test.yml @@ -6,7 +6,7 @@ files: - path: output/gatk4/test.bam - path: output/gatk4/versions.yml - md5sum: 03f3accdc3e3c392c1179213286a0b67 + md5sum: 381cdb2496b2fcc7bbc371a6e4156c7e - name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end command: nextflow run tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c tests/config/nextflow.config -c ./tests/modules/gatk4/fastqtosam/nextflow.config @@ -16,4 +16,4 @@ files: - path: output/gatk4/test.bam - path: output/gatk4/versions.yml - md5sum: 144e7118d5f277ad5fba863213c810b0 + md5sum: 1d07c90cbd31992c9ba003f02d1b3502 diff --git a/tests/modules/gatk4/gatherbqsrreports/test.yml b/tests/modules/gatk4/gatherbqsrreports/test.yml index 521f2197..576889de 100644 --- a/tests/modules/gatk4/gatherbqsrreports/test.yml +++ b/tests/modules/gatk4/gatherbqsrreports/test.yml @@ -7,7 +7,7 @@ - path: output/gatk4/test.table md5sum: 9603b69fdc3b5090de2e0dd78bfcc4bf - path: output/gatk4/versions.yml - md5sum: b53101f71b0763e80855703ba4e1f101 + md5sum: 8d52c5aaab73294e9ea5491b95f3e1e1 - name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports_multiple command: nextflow run tests/modules/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports_multiple -c tests/config/nextflow.config @@ -18,4 +18,4 @@ - path: output/gatk4/test.table md5sum: 0c1257eececf95db8ca378272d0f21f9 - path: output/gatk4/versions.yml - md5sum: 584a6ebf04f54abcfcf4c8255e13ff2a + md5sum: 91cad396b9f2045c3cd8c0f256672e80 diff --git a/tests/modules/gatk4/genomicsdbimport/test.yml b/tests/modules/gatk4/genomicsdbimport/test.yml index d1a8f073..5c4ea2bb 100644 --- a/tests/modules/gatk4/genomicsdbimport/test.yml +++ b/tests/modules/gatk4/genomicsdbimport/test.yml @@ -19,7 +19,7 @@ - path: output/gatk4/test/vidmap.json md5sum: 18d3f68bd2cb6f4474990507ff95017a - path: output/gatk4/versions.yml - md5sum: 6fffaf981f099659cf820277d1f3c606 + md5sum: 91f5c3e9529982f9c819860b403576ce - name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_get_intervalslist command: nextflow run tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_get_intervalslist -c tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config @@ -30,7 +30,7 @@ - path: output/gatk4/test.interval_list md5sum: 4c85812ac15fc1cd29711a851d23c0bf - path: output/gatk4/versions.yml - md5sum: 4a56022d6e08d54e8ba853637bf3b5f1 + md5sum: a898fe1cbc4acfa5936c0ffdcf121401 - path: output/untar/versions.yml md5sum: 8f080677b109aea2cfca50208b077534 @@ -55,6 +55,6 @@ - path: output/gatk4/test_genomicsdb/vidmap.json md5sum: 18d3f68bd2cb6f4474990507ff95017a - path: output/gatk4/versions.yml - md5sum: da6a815b7340683b1a56bdfd7e66d463 + md5sum: d87baa3f4218c5554cad3c008cb6cbc4 - path: output/untar/versions.yml md5sum: 9b2916aea9790bdf427c0cb38109110c diff --git a/tests/modules/gatk4/getpileupsummaries/test.yml b/tests/modules/gatk4/getpileupsummaries/test.yml index c032acf0..e3b25227 100644 --- a/tests/modules/gatk4/getpileupsummaries/test.yml +++ b/tests/modules/gatk4/getpileupsummaries/test.yml @@ -7,7 +7,7 @@ - path: output/gatk4/test.pileups.table md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469 - path: output/gatk4/versions.yml - md5sum: dd98374e3b5d35ddd1c6b3fa7e662dc5 + md5sum: 059123619f3ed8d4cd178c4390b81e69 - name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c tests/config/nextflow.config @@ -18,7 +18,7 @@ - path: output/gatk4/test.pileups.table md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469 - path: output/gatk4/versions.yml - md5sum: 080b6af7df182558aeab117668388d59 + md5sum: 76b5388b0c5b5762d8d33e34b23f181d - name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites_cram command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites_cram -c tests/config/nextflow.config @@ -29,4 +29,4 @@ - path: output/gatk4/test.pileups.table md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469 - path: output/gatk4/versions.yml - md5sum: 33458a9efa6d61c713af9f7b722d7134 + md5sum: 2fa51319c2b1d678ee00ab09512cf268 diff --git a/tests/modules/gatk4/indexfeaturefile/test.yml b/tests/modules/gatk4/indexfeaturefile/test.yml index 04c71ea2..938c2b91 100644 --- a/tests/modules/gatk4/indexfeaturefile/test.yml +++ b/tests/modules/gatk4/indexfeaturefile/test.yml @@ -15,7 +15,7 @@ - path: output/gatk4/genome.bed.gz.tbi md5sum: 4bc51e2351a6e83f20e13be75861f941 - path: output/gatk4/versions.yml - md5sum: 9eb24dc17c96971b7991b3e154279aa7 + md5sum: e5003204702f83aabdb4141272c704d2 - name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf -c tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config @@ -25,7 +25,7 @@ files: - path: output/gatk4/test.genome.vcf.idx - path: output/gatk4/versions.yml - md5sum: f76543e715342bf1fcdeb20385e01fe9 + md5sum: 08cd7c49cfb752fc2905f600106a0345 - name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf_gz command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf_gz -c tests/config/nextflow.config @@ -36,4 +36,4 @@ - path: output/gatk4/test.genome.vcf.gz.tbi md5sum: fedd68eaddf8d31257853d9da8325bd3 - path: output/gatk4/versions.yml - md5sum: a5d988cf62648f700ffac7257e72b2c0 + md5sum: b388d1681831a40264a7a27f67a8b247 diff --git a/tests/modules/gatk4/markduplicates/test.yml b/tests/modules/gatk4/markduplicates/test.yml index 333de7c9..7bf49b56 100644 --- a/tests/modules/gatk4/markduplicates/test.yml +++ b/tests/modules/gatk4/markduplicates/test.yml @@ -5,12 +5,12 @@ - gatk4/markduplicates files: - path: output/gatk4/test.bai - md5sum: c8f7a9e426c768577f88f59cb1336bf3 + md5sum: e9c125e82553209933883b4fe2b8d7c2 - path: output/gatk4/test.bam - md5sum: fba0c99a0b087c90113a210e4465f91b + md5sum: 2efd50b2e6b7fd9bdf242cd9e266cfa9 - path: output/gatk4/test.metrics - path: output/gatk4/versions.yml - md5sum: dacbab0e112d2403b09df138d4e62895 + md5sum: 0bc949aaa8792cd6c537cdaab0e2c145 - name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_bams -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config @@ -19,9 +19,9 @@ - gatk4/markduplicates files: - path: output/gatk4/test.bai - md5sum: 325932c51f6898b02dfec469c984ba28 + md5sum: bad71df9c876e72a5bc0a3e0fd755f92 - path: output/gatk4/test.bam - md5sum: f7cba8104e3a7024a5e00c02304f7dea + md5sum: 8187febc6108ffef7f907e89b9c091a4 - path: output/gatk4/test.metrics - path: output/gatk4/versions.yml - md5sum: 14d0d085df7d2f9e770578d92c329299 + md5sum: b10d63cf7b2b672915cb30cea081ccd5 diff --git a/tests/modules/gatk4/splitncigarreads/test.yml b/tests/modules/gatk4/splitncigarreads/test.yml index a18fbb04..059d5e75 100644 --- a/tests/modules/gatk4/splitncigarreads/test.yml +++ b/tests/modules/gatk4/splitncigarreads/test.yml @@ -5,6 +5,6 @@ - gatk4/splitncigarreads files: - path: output/gatk4/test.bam - md5sum: 1d54057d9f403fba2068ac1aaa4b8a28 + md5sum: ceed15c0bd64ff5c38d3816905933b0b - path: output/gatk4/versions.yml - md5sum: f0f29af552075dc6bf8a13028e09f8e4 + md5sum: 27fceace2528a905ddca2b4db47c4bf5 diff --git a/tests/modules/gatk4/variantrecalibrator/main.nf b/tests/modules/gatk4/variantrecalibrator/main.nf index bbc1dff5..be7004e7 100644 --- a/tests/modules/gatk4/variantrecalibrator/main.nf +++ b/tests/modules/gatk4/variantrecalibrator/main.nf @@ -2,7 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK4_VARIANTRECALIBRATOR } from '../../../../modules/gatk4/variantrecalibrator/main.nf' +include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY } from '../../../../modules/gatk4/variantrecalibrator/main.nf' +include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY } from '../../../../modules/gatk4/variantrecalibrator/main.nf' workflow test_gatk4_variantrecalibrator { @@ -14,7 +15,6 @@ workflow test_gatk4_variantrecalibrator { fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) - allelespecific = false resources = [ [ file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true), @@ -35,11 +35,8 @@ workflow test_gatk4_variantrecalibrator { 'dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' ] ] - annotation = ['QD', 'MQ', 'FS', 'SOR'] - mode = 'SNP' - create_rscript = false - GATK4_VARIANTRECALIBRATOR ( input, fasta, fai, dict, allelespecific, resources, annotation, mode, create_rscript) + GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY ( input, fasta, fai, dict, resources) } workflow test_gatk4_variantrecalibrator_allele_specific { @@ -52,7 +49,6 @@ workflow test_gatk4_variantrecalibrator_allele_specific { fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) - allelespecific = true resources = [ [ file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true), @@ -73,9 +69,6 @@ workflow test_gatk4_variantrecalibrator_allele_specific { 'dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' ] ] - annotation = ['QD', 'MQ', 'FS'] - mode = 'SNP' - create_rscript = false - GATK4_VARIANTRECALIBRATOR ( input, fasta, fai, dict, allelespecific, resources, annotation, mode, create_rscript) + GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY ( input, fasta, fai, dict, resources) } diff --git a/tests/modules/gatk4/variantrecalibrator/nextflow.config b/tests/modules/gatk4/variantrecalibrator/nextflow.config index 19934e76..69be3b9c 100644 --- a/tests/modules/gatk4/variantrecalibrator/nextflow.config +++ b/tests/modules/gatk4/variantrecalibrator/nextflow.config @@ -1,5 +1,11 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + withName: GATK4_VARIANTRECALIBRATOR { + ext.args = '--mode SNP -an QD -an MQ -an FS -an SOR' + } -} \ No newline at end of file + withName: GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY { + ext.args = '--mode SNP -an QD -an MQ -an FS -AS' + } +}