From 50eafb19c689bca7747a6d44b8e7a555ba172f4b Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Mon, 20 Dec 2021 17:10:49 +0100 Subject: [PATCH] Update version for log4j vulnerability (#1176) * Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead --- modules/gatk4/applybqsr/main.nf | 6 +- modules/gatk4/applyvqsr/main.nf | 6 +- modules/gatk4/baserecalibrator/main.nf | 6 +- modules/gatk4/bedtointervallist/main.nf | 6 +- modules/gatk4/calculatecontamination/main.nf | 12 ++-- .../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 +- tests/config/test_data.config | 15 ++++- tests/modules/gatk4/applybqsr/test.yml | 24 ++++--- tests/modules/gatk4/applyvqsr/test.yml | 8 ++- .../gatk4/calculatecontamination/test.yml | 34 ++++++---- tests/modules/gatk4/fastqtosam/test.yml | 12 ++-- tests/modules/gatk4/filtermutectcalls/main.nf | 18 ++--- .../modules/gatk4/filtermutectcalls/test.yml | 9 +-- .../modules/gatk4/gatherbqsrreports/test.yml | 4 +- tests/modules/gatk4/genomicsdbimport/test.yml | 26 +++++--- tests/modules/gatk4/genotypegvcfs/test.yml | 18 ++--- .../modules/gatk4/getpileupsummaries/main.nf | 10 +-- .../modules/gatk4/getpileupsummaries/test.yml | 4 +- tests/modules/gatk4/indexfeaturefile/test.yml | 24 +++---- tests/modules/gatk4/markduplicates/test.yml | 16 +++-- tests/modules/gatk4/mutect2/main.nf | 66 ++++++++++--------- tests/modules/gatk4/mutect2/test.yml | 8 +-- tests/modules/gatk4/splitncigarreads/test.yml | 6 +- 43 files changed, 253 insertions(+), 211 deletions(-) diff --git a/modules/gatk4/applybqsr/main.nf b/modules/gatk4/applybqsr/main.nf index 3cc69ddf..20294c27 100644 --- a/modules/gatk4/applybqsr/main.nf +++ b/modules/gatk4/applybqsr/main.nf @@ -2,10 +2,10 @@ process GATK4_APPLYBQSR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(bqsr_table) diff --git a/modules/gatk4/applyvqsr/main.nf b/modules/gatk4/applyvqsr/main.nf index 89f79f42..9e61ba4b 100644 --- a/modules/gatk4/applyvqsr/main.nf +++ b/modules/gatk4/applyvqsr/main.nf @@ -2,10 +2,10 @@ process GATK4_APPLYVQSR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi), path(recal), path(recalidx), path(tranches) diff --git a/modules/gatk4/baserecalibrator/main.nf b/modules/gatk4/baserecalibrator/main.nf index 17b37943..8a45d6e2 100644 --- a/modules/gatk4/baserecalibrator/main.nf +++ b/modules/gatk4/baserecalibrator/main.nf @@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/gatk4/bedtointervallist/main.nf b/modules/gatk4/bedtointervallist/main.nf index 2f6266b9..76d0f8a4 100644 --- a/modules/gatk4/bedtointervallist/main.nf +++ b/modules/gatk4/bedtointervallist/main.nf @@ -2,10 +2,10 @@ process GATK4_BEDTOINTERVALLIST { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(bed) diff --git a/modules/gatk4/calculatecontamination/main.nf b/modules/gatk4/calculatecontamination/main.nf index 8840356a..7fc88076 100644 --- a/modules/gatk4/calculatecontamination/main.nf +++ b/modules/gatk4/calculatecontamination/main.nf @@ -2,19 +2,19 @@ process GATK4_CALCULATECONTAMINATION { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(pileup), path(matched) val segmentout output: - tuple val(meta), path('*.contamination.table') , emit: contamination - tuple val(meta), path('*.segmentation.table') , optional:true, emit: segmentation - path "versions.yml" , emit: versions + tuple val(meta), path('*.contamination.table'), emit: contamination + tuple val(meta), path('*.segmentation.table') , emit: segmentation, optional:true + path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' diff --git a/modules/gatk4/createsequencedictionary/main.nf b/modules/gatk4/createsequencedictionary/main.nf index e8f32106..4d82a643 100644 --- a/modules/gatk4/createsequencedictionary/main.nf +++ b/modules/gatk4/createsequencedictionary/main.nf @@ -2,10 +2,10 @@ process GATK4_CREATESEQUENCEDICTIONARY { tag "$fasta" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: path fasta diff --git a/modules/gatk4/createsomaticpanelofnormals/main.nf b/modules/gatk4/createsomaticpanelofnormals/main.nf index ff345f75..c094084f 100644 --- a/modules/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/gatk4/createsomaticpanelofnormals/main.nf @@ -2,10 +2,10 @@ process GATK4_CREATESOMATICPANELOFNORMALS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(genomicsdb) diff --git a/modules/gatk4/estimatelibrarycomplexity/main.nf b/modules/gatk4/estimatelibrarycomplexity/main.nf index c17dba09..78079c20 100644 --- a/modules/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/gatk4/estimatelibrarycomplexity/main.nf @@ -2,10 +2,10 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(cram) diff --git a/modules/gatk4/fastqtosam/main.nf b/modules/gatk4/fastqtosam/main.nf index a55ba709..2c13890f 100644 --- a/modules/gatk4/fastqtosam/main.nf +++ b/modules/gatk4/fastqtosam/main.nf @@ -2,10 +2,10 @@ process GATK4_FASTQTOSAM { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/gatk4/filtermutectcalls/main.nf b/modules/gatk4/filtermutectcalls/main.nf index 6a1d9b3a..e68d01db 100644 --- a/modules/gatk4/filtermutectcalls/main.nf +++ b/modules/gatk4/filtermutectcalls/main.nf @@ -2,10 +2,10 @@ process GATK4_FILTERMUTECTCALLS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--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 1567f9aa..721f5634 100644 --- a/modules/gatk4/gatherbqsrreports/main.nf +++ b/modules/gatk4/gatherbqsrreports/main.nf @@ -2,10 +2,10 @@ process GATK4_GATHERBQSRREPORTS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_1': - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(recal_table) diff --git a/modules/gatk4/genomicsdbimport/main.nf b/modules/gatk4/genomicsdbimport/main.nf index 2751173b..f1a606cb 100644 --- a/modules/gatk4/genomicsdbimport/main.nf +++ b/modules/gatk4/genomicsdbimport/main.nf @@ -2,10 +2,10 @@ process GATK4_GENOMICSDBIMPORT { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--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 50a6e188..b1c15a5e 100644 --- a/modules/gatk4/genotypegvcfs/main.nf +++ b/modules/gatk4/genotypegvcfs/main.nf @@ -2,10 +2,10 @@ process GATK4_GENOTYPEGVCFS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(gvcf), path(gvcf_index) diff --git a/modules/gatk4/getpileupsummaries/main.nf b/modules/gatk4/getpileupsummaries/main.nf index 361974e8..896e23bd 100644 --- a/modules/gatk4/getpileupsummaries/main.nf +++ b/modules/gatk4/getpileupsummaries/main.nf @@ -2,10 +2,10 @@ process GATK4_GETPILEUPSUMMARIES { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/gatk4/haplotypecaller/main.nf b/modules/gatk4/haplotypecaller/main.nf index e00f1e58..d6cf514d 100644 --- a/modules/gatk4/haplotypecaller/main.nf +++ b/modules/gatk4/haplotypecaller/main.nf @@ -2,10 +2,10 @@ process GATK4_HAPLOTYPECALLER { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/gatk4/indexfeaturefile/main.nf b/modules/gatk4/indexfeaturefile/main.nf index cc6c663e..63633e5f 100644 --- a/modules/gatk4/indexfeaturefile/main.nf +++ b/modules/gatk4/indexfeaturefile/main.nf @@ -2,10 +2,10 @@ process GATK4_INDEXFEATUREFILE { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0' : - 'quay.io/biocontainers/gatk4:4.2.0.0--0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(feature_file) diff --git a/modules/gatk4/intervallisttools/main.nf b/modules/gatk4/intervallisttools/main.nf index b813d844..b1881932 100644 --- a/modules/gatk4/intervallisttools/main.nf +++ b/modules/gatk4/intervallisttools/main.nf @@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOOLS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(interval_list) diff --git a/modules/gatk4/learnreadorientationmodel/main.nf b/modules/gatk4/learnreadorientationmodel/main.nf index 0c2f09d2..961b6a75 100644 --- a/modules/gatk4/learnreadorientationmodel/main.nf +++ b/modules/gatk4/learnreadorientationmodel/main.nf @@ -2,10 +2,10 @@ process GATK4_LEARNREADORIENTATIONMODEL { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(f1r2) diff --git a/modules/gatk4/markduplicates/main.nf b/modules/gatk4/markduplicates/main.nf index 8bdb2c0a..5f6f127e 100644 --- a/modules/gatk4/markduplicates/main.nf +++ b/modules/gatk4/markduplicates/main.nf @@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(bams) diff --git a/modules/gatk4/mergebamalignment/main.nf b/modules/gatk4/mergebamalignment/main.nf index a0f54976..b13b9ae8 100644 --- a/modules/gatk4/mergebamalignment/main.nf +++ b/modules/gatk4/mergebamalignment/main.nf @@ -2,10 +2,10 @@ process GATK4_MERGEBAMALIGNMENT { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(aligned) diff --git a/modules/gatk4/mergevcfs/main.nf b/modules/gatk4/mergevcfs/main.nf index 1fcce485..9158a242 100644 --- a/modules/gatk4/mergevcfs/main.nf +++ b/modules/gatk4/mergevcfs/main.nf @@ -2,10 +2,10 @@ process GATK4_MERGEVCFS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(vcfs) diff --git a/modules/gatk4/mutect2/main.nf b/modules/gatk4/mutect2/main.nf index 414c7705..1abf44ea 100644 --- a/modules/gatk4/mutect2/main.nf +++ b/modules/gatk4/mutect2/main.nf @@ -2,10 +2,10 @@ process GATK4_MUTECT2 { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta) , path(input) , path(input_index) , val(which_norm) diff --git a/modules/gatk4/revertsam/main.nf b/modules/gatk4/revertsam/main.nf index 0713d7ca..585d2063 100644 --- a/modules/gatk4/revertsam/main.nf +++ b/modules/gatk4/revertsam/main.nf @@ -2,10 +2,10 @@ process GATK4_REVERTSAM { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/gatk4/samtofastq/main.nf b/modules/gatk4/samtofastq/main.nf index 0afb7ef3..9b73299f 100644 --- a/modules/gatk4/samtofastq/main.nf +++ b/modules/gatk4/samtofastq/main.nf @@ -2,10 +2,10 @@ process GATK4_SAMTOFASTQ { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/gatk4/splitncigarreads/main.nf b/modules/gatk4/splitncigarreads/main.nf index 6daed954..c27c393f 100644 --- a/modules/gatk4/splitncigarreads/main.nf +++ b/modules/gatk4/splitncigarreads/main.nf @@ -2,10 +2,10 @@ process GATK4_SPLITNCIGARREADS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/gatk4/variantfiltration/main.nf b/modules/gatk4/variantfiltration/main.nf index efe245cc..32e4aae1 100644 --- a/modules/gatk4/variantfiltration/main.nf +++ b/modules/gatk4/variantfiltration/main.nf @@ -2,10 +2,10 @@ process GATK4_VARIANTFILTRATION { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(vcf), path(vcf_tbi) diff --git a/tests/config/test_data.config b/tests/config/test_data.config index ee1ba0d8..fde5dc42 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -118,6 +118,7 @@ params { genome_21_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" genome_21_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" genome_21_dict = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict" + genome_21_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list" dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" dbsnp_146_hg38_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" @@ -125,6 +126,9 @@ params { gnomad_r2_1_1_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi" mills_and_1000g_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz" mills_and_1000g_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi" + syntheticvcf_short_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz" + syntheticvcf_short_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi" + hapmap_3_3_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz" hapmap_3_3_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi" res_1000g_omni2_5_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz" @@ -133,9 +137,10 @@ params { res_1000g_phase1_snps_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi" dbsnp_138_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz" dbsnp_138_hg38_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi" - - syntheticvcf_short_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz" - syntheticvcf_short_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi" + gnomad_r2_1_1_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz" + gnomad_r2_1_1_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi" + mills_and_1000g_indels_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz" + mills_and_1000g_indels_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi" index_salmon = "${test_data_dir}/genomics/homo_sapiens/genome/index/salmon" repeat_expansions = "${test_data_dir}/genomics/homo_sapiens/genome/loci/repeat_expansions.json" @@ -175,6 +180,10 @@ params { test2_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam" test2_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam" + + mitochon_standin_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam" + mitochon_standin_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai" + test_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram" test_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai" test_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram" diff --git a/tests/modules/gatk4/applybqsr/test.yml b/tests/modules/gatk4/applybqsr/test.yml index d0b07d94..af29be71 100644 --- a/tests/modules/gatk4/applybqsr/test.yml +++ b/tests/modules/gatk4/applybqsr/test.yml @@ -1,26 +1,32 @@ - name: gatk4 applybqsr test_gatk4_applybqsr - command: nextflow run ./tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config + command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config tags: - - gatk4/applybqsr - gatk4 + - gatk4/applybqsr files: - path: output/gatk4/test.bam - md5sum: af56f5dd81b95070079d54670507f530 + md5sum: 8fe7c4b5fcfb72d24ed8102eb26e42fb + - path: output/gatk4/versions.yml + md5sum: 8a2fb7c7e38f24d3fefd5e84da701b00 - 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 + command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config tags: - - gatk4/applybqsr - gatk4 + - gatk4/applybqsr files: - path: output/gatk4/test.bam - md5sum: 0cbfa4be143e988d56ce741b5077510e + md5sum: a7a1d1373ac1529abbc5e05359718ab1 + - path: output/gatk4/versions.yml + md5sum: 550eecbb88887fadf8c62c5992ae48af - 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 + command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_cram -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config tags: - - gatk4/applybqsr - gatk4 + - gatk4/applybqsr files: - path: output/gatk4/test.bam - md5sum: 720ef7453fc3c9def18bbe396062346c + md5sum: a333f80284a89a8daab28d3686a0b365 + - path: output/gatk4/versions.yml + md5sum: 57933f27b3a31b05af3f7c248d365396 diff --git a/tests/modules/gatk4/applyvqsr/test.yml b/tests/modules/gatk4/applyvqsr/test.yml index e870bed3..577da79d 100644 --- a/tests/modules/gatk4/applyvqsr/test.yml +++ b/tests/modules/gatk4/applyvqsr/test.yml @@ -1,17 +1,21 @@ - name: gatk4 applyvqsr test_gatk4_applyvqsr command: nextflow run tests/modules/gatk4/applyvqsr -entry test_gatk4_applyvqsr -c tests/config/nextflow.config -c ./tests/modules/gatk4/applyvqsr/nextflow.config tags: - - gatk4 - gatk4/applyvqsr + - gatk4 files: - path: output/gatk4/test.vcf.gz - path: output/gatk4/test.vcf.gz.tbi + - path: output/gatk4/versions.yml + md5sum: 984c932ee9a5683b18e22a369aa5c9e7 - 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 tags: - - gatk4 - gatk4/applyvqsr + - gatk4 files: - path: output/gatk4/test.vcf.gz - path: output/gatk4/test.vcf.gz.tbi + - path: output/gatk4/versions.yml + md5sum: 3b55f26c94c5f145f10ef4c5f83ec3cc diff --git a/tests/modules/gatk4/calculatecontamination/test.yml b/tests/modules/gatk4/calculatecontamination/test.yml index 0c489bff..9370ffd4 100644 --- a/tests/modules/gatk4/calculatecontamination/test.yml +++ b/tests/modules/gatk4/calculatecontamination/test.yml @@ -1,28 +1,34 @@ - name: gatk4 calculatecontamination test_gatk4_calculatecontamination_tumor_only - command: nextflow run ./tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_tumor_only -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config + command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_tumor_only -c tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config tags: - - gatk4/calculatecontamination - gatk4 + - gatk4/calculatecontamination files: - - path: output/gatk4/test.contamination.table - md5sum: 5fdcf1728cf98985ce31c038eb24e05c + - path: output/gatk4/test.contamination.table + md5sum: 46c708c943b453da89a3da08acfdb2a7 + - path: output/gatk4/versions.yml + md5sum: 6f2396e71389cdfd184f91222c24fe8d - 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 + 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 tags: - - gatk4/calculatecontamination - gatk4 + - gatk4/calculatecontamination files: - - path: output/gatk4/test.contamination.table - md5sum: 5fdcf1728cf98985ce31c038eb24e05c + - path: output/gatk4/test.contamination.table + md5sum: 46c708c943b453da89a3da08acfdb2a7 + - path: output/gatk4/versions.yml + md5sum: 26863fa1e7e7d50d1a10761eced26062 - 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 + command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_segmentation -c tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config tags: - - gatk4/calculatecontamination - gatk4 + - gatk4/calculatecontamination files: - - path: output/gatk4/test.contamination.table - md5sum: 5fdcf1728cf98985ce31c038eb24e05c - - path: output/gatk4/test.segmentation.table - md5sum: 91f28bfe4727a3256810927fc5eba92f + - path: output/gatk4/test.contamination.table + md5sum: 46c708c943b453da89a3da08acfdb2a7 + - path: output/gatk4/test.segmentation.table + md5sum: f4643d9319bde4efbfbe516d6fb13052 + - path: output/gatk4/versions.yml + md5sum: 8b1191953ff20660e06e2a5d79e96b02 diff --git a/tests/modules/gatk4/fastqtosam/test.yml b/tests/modules/gatk4/fastqtosam/test.yml index d5d23f94..912633b5 100644 --- a/tests/modules/gatk4/fastqtosam/test.yml +++ b/tests/modules/gatk4/fastqtosam/test.yml @@ -1,17 +1,19 @@ - name: gatk4 fastqtosam test_gatk4_fastqtosam_single_end - command: nextflow run ./tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/fastqtosam/nextflow.config + command: nextflow run tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c tests/config/nextflow.config -c ./tests/modules/gatk4/fastqtosam/nextflow.config tags: - - gatk4/fastqtosam - gatk4 + - gatk4/fastqtosam files: - path: output/gatk4/test.bam - md5sum: 0a0d308b219837977b8df9daa26db7de + - path: output/gatk4/versions.yml + md5sum: db3fa4b463427b08e32a5d8264be59c1 - 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 + 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 tags: - gatk4 - gatk4/fastqtosam files: - path: output/gatk4/test.bam - md5sum: 0a0d308b219837977b8df9daa26db7de + - path: output/gatk4/versions.yml + md5sum: f4e35e46a29d8faebda5e852f9d0a132 diff --git a/tests/modules/gatk4/filtermutectcalls/main.nf b/tests/modules/gatk4/filtermutectcalls/main.nf index fa0acff9..d7d0dd8c 100644 --- a/tests/modules/gatk4/filtermutectcalls/main.nf +++ b/tests/modules/gatk4/filtermutectcalls/main.nf @@ -17,9 +17,9 @@ workflow test_gatk4_filtermutectcalls_base { [] ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + 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) GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict ) } @@ -37,9 +37,9 @@ workflow test_gatk4_filtermutectcalls_with_files { [] ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + 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) GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict ) } @@ -57,9 +57,9 @@ workflow test_gatk4_filtermutectcalls_use_val { '20.0' ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + 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) GATK4_FILTERMUTECTCALLS ( input, fasta, fai, dict ) } diff --git a/tests/modules/gatk4/filtermutectcalls/test.yml b/tests/modules/gatk4/filtermutectcalls/test.yml index 72504e66..12cf4e69 100644 --- a/tests/modules/gatk4/filtermutectcalls/test.yml +++ b/tests/modules/gatk4/filtermutectcalls/test.yml @@ -6,9 +6,8 @@ files: - path: output/gatk4/test.filtered.vcf.gz - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv - md5sum: 98e1b87a52999eb8f429ef4a7877eb3f + md5sum: 55f228e5520c8b9fbac017d3a3a6c5fd - path: output/gatk4/test.filtered.vcf.gz.tbi - md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4 - name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_with_files command: nextflow run ./tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_with_files -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/filtermutectcalls/nextflow.config @@ -18,9 +17,8 @@ files: - path: output/gatk4/test.filtered.vcf.gz - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv - md5sum: 98e1b87a52999eb8f429ef4a7877eb3f + md5sum: 9ae27fbd04af1a2ea574e2ff1c3a683b - path: output/gatk4/test.filtered.vcf.gz.tbi - md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4 - name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_use_val command: nextflow run ./tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_use_val -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/filtermutectcalls/nextflow.config @@ -30,6 +28,5 @@ files: - path: output/gatk4/test.filtered.vcf.gz - path: output/gatk4/test.filtered.vcf.gz.filteringStats.tsv - md5sum: 98e1b87a52999eb8f429ef4a7877eb3f + md5sum: 95cc3e37705bd3b97a292c5d46ab82f3 - path: output/gatk4/test.filtered.vcf.gz.tbi - md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4 diff --git a/tests/modules/gatk4/gatherbqsrreports/test.yml b/tests/modules/gatk4/gatherbqsrreports/test.yml index 76c90120..38b8cf54 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: 50238fd0f3b6f4efb2b5335b6324f905 + md5sum: 2fa1214574359aa7c4e2212efbae3714 - 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: c6ce163062dd3609848fc5bc10660427 + md5sum: 92c17a728cef6d458491bcec6dac3e0c diff --git a/tests/modules/gatk4/genomicsdbimport/test.yml b/tests/modules/gatk4/genomicsdbimport/test.yml index 94a1a35e..059a561a 100644 --- a/tests/modules/gatk4/genomicsdbimport/test.yml +++ b/tests/modules/gatk4/genomicsdbimport/test.yml @@ -1,8 +1,8 @@ - name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_create_genomicsdb - command: nextflow run ./tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_create_genomicsdb -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config + command: nextflow run tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_create_genomicsdb -c tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config tags: - - gatk4/genomicsdbimport - gatk4 + - gatk4/genomicsdbimport files: - path: output/gatk4/test/__tiledb_workspace.tdb md5sum: d41d8cd98f00b204e9800998ecf8427e @@ -18,21 +18,27 @@ - "FORMAT=