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Log4j again (#1202)

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* Log4j again

* Update checksums
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FriederikeHanssen 2022-01-12 13:55:54 +01:00 committed by GitHub
parent 05ba4d901d
commit 598d7abdb2
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36 changed files with 111 additions and 111 deletions
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6
modules/gatk4/applybqsr/main.nf
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@ -2,10 +2,10 @@ process GATK4_APPLYBQSR {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)

6
modules/gatk4/applyvqsr/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_APPLYVQSR {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(vcf), path(tbi), path(recal), path(recalidx), path(tranches) tuple val(meta), path(vcf), path(tbi), path(recal), path(recalidx), path(tranches)

6
modules/gatk4/baserecalibrator/main.nf
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@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(input), path(input_index), path(intervals) tuple val(meta), path(input), path(input_index), path(intervals)

6
modules/gatk4/bedtointervallist/main.nf
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@ -2,10 +2,10 @@ process GATK4_BEDTOINTERVALLIST {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bed) tuple val(meta), path(bed)

6
modules/gatk4/calculatecontamination/main.nf
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@ -2,10 +2,10 @@ process GATK4_CALCULATECONTAMINATION {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(pileup), path(matched) tuple val(meta), path(pileup), path(matched)

6
modules/gatk4/createsequencedictionary/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_CREATESEQUENCEDICTIONARY {
tag "$fasta" tag "$fasta"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
path fasta path fasta

6
modules/gatk4/createsomaticpanelofnormals/main.nf
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@ -2,10 +2,10 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(genomicsdb) tuple val(meta), path(genomicsdb)

6
modules/gatk4/estimatelibrarycomplexity/main.nf
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@ -2,10 +2,10 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(cram) tuple val(meta), path(cram)

6
modules/gatk4/fastqtosam/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_FASTQTOSAM {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)

6
modules/gatk4/filtermutectcalls/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_FILTERMUTECTCALLS {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(vcf), path(tbi), path(stats), path(orientationbias), path(segmentation), path(contaminationfile), val(contaminationest) tuple val(meta), path(vcf), path(tbi), path(stats), path(orientationbias), path(segmentation), path(contaminationfile), val(contaminationest)

6
modules/gatk4/gatherbqsrreports/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_GATHERBQSRREPORTS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(recal_table) tuple val(meta), path(recal_table)

6
modules/gatk4/genomicsdbimport/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_GENOMICSDBIMPORT {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(vcf), path(tbi), path(intervalfile), val(intervalval), path(wspace) tuple val(meta), path(vcf), path(tbi), path(intervalfile), val(intervalval), path(wspace)

6
modules/gatk4/genotypegvcfs/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_GENOTYPEGVCFS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(gvcf), path(gvcf_index), path(intervals) tuple val(meta), path(gvcf), path(gvcf_index), path(intervals)

6
modules/gatk4/getpileupsummaries/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_GETPILEUPSUMMARIES {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam), path(bai) tuple val(meta), path(bam), path(bai)

6
modules/gatk4/haplotypecaller/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_HAPLOTYPECALLER {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(input), path(input_index), path(intervals) tuple val(meta), path(input), path(input_index), path(intervals)

6
modules/gatk4/indexfeaturefile/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_INDEXFEATUREFILE {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(feature_file) tuple val(meta), path(feature_file)

6
modules/gatk4/intervallisttools/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOOLS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(interval_list) tuple val(meta), path(interval_list)

6
modules/gatk4/learnreadorientationmodel/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_LEARNREADORIENTATIONMODEL {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(f1r2) tuple val(meta), path(f1r2)

6
modules/gatk4/markduplicates/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bams) tuple val(meta), path(bams)

6
modules/gatk4/mergebamalignment/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_MERGEBAMALIGNMENT {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(aligned) tuple val(meta), path(aligned)

6
modules/gatk4/mergevcfs/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_MERGEVCFS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(vcfs) tuple val(meta), path(vcfs)

6
modules/gatk4/mutect2/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_MUTECT2 {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta) , path(input) , path(input_index) , val(which_norm) tuple val(meta) , path(input) , path(input_index) , val(which_norm)

6
modules/gatk4/revertsam/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_REVERTSAM {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
modules/gatk4/samtofastq/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_SAMTOFASTQ {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
modules/gatk4/splitncigarreads/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_SPLITNCIGARREADS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
modules/gatk4/variantfiltration/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_VARIANTFILTRATION {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(vcf), path(vcf_tbi) tuple val(meta), path(vcf), path(vcf_tbi)

8
modules/gatk4/variantrecalibrator/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_VARIANTRECALIBRATOR {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(vcf) , path(tbi) tuple val(meta), path(vcf) , path(tbi)

12
tests/modules/gatk4/applybqsr/test.yml
View file

@ -5,9 +5,9 @@
- gatk4/applybqsr - gatk4/applybqsr
files: files:
- path: output/gatk4/test.bam - path: output/gatk4/test.bam
md5sum: 8fe7c4b5fcfb72d24ed8102eb26e42fb md5sum: 908825edf1f229a072f91d8b753d95dd
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: 8a2fb7c7e38f24d3fefd5e84da701b00 md5sum: b65c46529ae9658db0c596cbc26505c2
- name: gatk4 applybqsr test_gatk4_applybqsr_intervals - 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
@ -16,9 +16,9 @@
- gatk4/applybqsr - gatk4/applybqsr
files: files:
- path: output/gatk4/test.bam - path: output/gatk4/test.bam
md5sum: a7a1d1373ac1529abbc5e05359718ab1 md5sum: 50f8a79c7d528e02470416f81eb582bc
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: 550eecbb88887fadf8c62c5992ae48af md5sum: 17c8a40b3537e3400edebd1826d28385
- name: gatk4 applybqsr test_gatk4_applybqsr_cram - 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
@ -27,6 +27,6 @@
- gatk4/applybqsr - gatk4/applybqsr
files: files:
- path: output/gatk4/test.cram - path: output/gatk4/test.cram
md5sum: b7659b3b2adaabbe73658dc059dbfdf6 md5sum: cd8d4ba6181f714e74641adeb2f9aa1d
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: 57933f27b3a31b05af3f7c248d365396 md5sum: 35218922e1929c699ea64de9f4c29fb5

4
tests/modules/gatk4/applyvqsr/test.yml
View file

@ -7,7 +7,7 @@
- path: output/gatk4/test.vcf.gz - path: output/gatk4/test.vcf.gz
- path: output/gatk4/test.vcf.gz.tbi - path: output/gatk4/test.vcf.gz.tbi
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: 984c932ee9a5683b18e22a369aa5c9e7 md5sum: 524a78cdfa56c8b09a4ff3f4cb278261
- name: gatk4 applyvqsr test_gatk4_applyvqsr_allele_specific - 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 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
- path: output/gatk4/test.vcf.gz.tbi - path: output/gatk4/test.vcf.gz.tbi
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: 3b55f26c94c5f145f10ef4c5f83ec3cc md5sum: 7a3c6e97628bd1f5f4e7fd429bf74a8e

6
tests/modules/gatk4/calculatecontamination/test.yml
View file

@ -7,7 +7,7 @@
- path: output/gatk4/test.contamination.table - path: output/gatk4/test.contamination.table
md5sum: 46c708c943b453da89a3da08acfdb2a7 md5sum: 46c708c943b453da89a3da08acfdb2a7
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: 6f2396e71389cdfd184f91222c24fe8d md5sum: 79575dc2e6a7f0361f2d8b090c496070
- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_matched_pair - 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
@ -18,7 +18,7 @@
- path: output/gatk4/test.contamination.table - path: output/gatk4/test.contamination.table
md5sum: 46c708c943b453da89a3da08acfdb2a7 md5sum: 46c708c943b453da89a3da08acfdb2a7
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: 26863fa1e7e7d50d1a10761eced26062 md5sum: 733f15ef7eb504daec9fd8cd9beef71a
- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_segmentation - 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
@ -31,4 +31,4 @@
- path: output/gatk4/test.segmentation.table - path: output/gatk4/test.segmentation.table
md5sum: f4643d9319bde4efbfbe516d6fb13052 md5sum: f4643d9319bde4efbfbe516d6fb13052
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: 8b1191953ff20660e06e2a5d79e96b02 md5sum: 5396e33146addbe4a59d0f30cb573a3a

4
tests/modules/gatk4/fastqtosam/test.yml
View file

@ -6,7 +6,7 @@
files: files:
- path: output/gatk4/test.bam - path: output/gatk4/test.bam
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: db3fa4b463427b08e32a5d8264be59c1 md5sum: 03f3accdc3e3c392c1179213286a0b67
- name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end - 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
@ -16,4 +16,4 @@
files: files:
- path: output/gatk4/test.bam - path: output/gatk4/test.bam
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: f4e35e46a29d8faebda5e852f9d0a132 md5sum: 144e7118d5f277ad5fba863213c810b0

4
tests/modules/gatk4/gatherbqsrreports/test.yml
View file

@ -7,7 +7,7 @@
- path: output/gatk4/test.table - path: output/gatk4/test.table
md5sum: 9603b69fdc3b5090de2e0dd78bfcc4bf md5sum: 9603b69fdc3b5090de2e0dd78bfcc4bf
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: 2fa1214574359aa7c4e2212efbae3714 md5sum: b53101f71b0763e80855703ba4e1f101
- name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports_multiple - name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports_multiple
command: nextflow run tests/modules/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports_multiple -c tests/config/nextflow.config 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 - path: output/gatk4/test.table
md5sum: 0c1257eececf95db8ca378272d0f21f9 md5sum: 0c1257eececf95db8ca378272d0f21f9
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: 92c17a728cef6d458491bcec6dac3e0c md5sum: 584a6ebf04f54abcfcf4c8255e13ff2a

6
tests/modules/gatk4/genomicsdbimport/test.yml
View file

@ -19,7 +19,7 @@
- path: output/gatk4/test/vidmap.json - path: output/gatk4/test/vidmap.json
md5sum: 18d3f68bd2cb6f4474990507ff95017a md5sum: 18d3f68bd2cb6f4474990507ff95017a
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: 92e9e7db68d22df72adc02e59fab1eb7 md5sum: 6fffaf981f099659cf820277d1f3c606
- name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_get_intervalslist - 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 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 - path: output/gatk4/test.interval_list
md5sum: 4c85812ac15fc1cd29711a851d23c0bf md5sum: 4c85812ac15fc1cd29711a851d23c0bf
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: b3fcd07c2f498a2ad503912524d74294 md5sum: 4a56022d6e08d54e8ba853637bf3b5f1
- path: output/untar/versions.yml - path: output/untar/versions.yml
md5sum: 8f080677b109aea2cfca50208b077534 md5sum: 8f080677b109aea2cfca50208b077534
@ -55,6 +55,6 @@
- path: output/gatk4/test_genomicsdb/vidmap.json - path: output/gatk4/test_genomicsdb/vidmap.json
md5sum: 18d3f68bd2cb6f4474990507ff95017a md5sum: 18d3f68bd2cb6f4474990507ff95017a
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: f204d259538a490b40c1fe787a3d6602 md5sum: da6a815b7340683b1a56bdfd7e66d463
- path: output/untar/versions.yml - path: output/untar/versions.yml
md5sum: 9b2916aea9790bdf427c0cb38109110c md5sum: 9b2916aea9790bdf427c0cb38109110c

6
tests/modules/gatk4/indexfeaturefile/test.yml
View file

@ -15,7 +15,7 @@
- path: output/gatk4/genome.bed.gz.tbi - path: output/gatk4/genome.bed.gz.tbi
md5sum: 4bc51e2351a6e83f20e13be75861f941 md5sum: 4bc51e2351a6e83f20e13be75861f941
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: e574bd51e4c6d6ded5dcf3cd865dbf4a md5sum: 9eb24dc17c96971b7991b3e154279aa7
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf - 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 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: files:
- path: output/gatk4/test.genome.vcf.idx - path: output/gatk4/test.genome.vcf.idx
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: fee70d33f4379ced035d8e851a3e08c6 md5sum: f76543e715342bf1fcdeb20385e01fe9
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf_gz - 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 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 - path: output/gatk4/test.genome.vcf.gz.tbi
md5sum: fedd68eaddf8d31257853d9da8325bd3 md5sum: fedd68eaddf8d31257853d9da8325bd3
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: 29bddb019f0fe04218cfc07f8203e022 md5sum: a5d988cf62648f700ffac7257e72b2c0

12
tests/modules/gatk4/markduplicates/test.yml
View file

@ -5,12 +5,12 @@
- gatk4/markduplicates - gatk4/markduplicates
files: files:
- path: output/gatk4/test.bai - path: output/gatk4/test.bai
md5sum: e9c125e82553209933883b4fe2b8d7c2 md5sum: c8f7a9e426c768577f88f59cb1336bf3
- path: output/gatk4/test.bam - path: output/gatk4/test.bam
md5sum: 1c6b1372121eddccd086456aa1c174bf md5sum: fba0c99a0b087c90113a210e4465f91b
- path: output/gatk4/test.metrics - path: output/gatk4/test.metrics
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: 0e46677bdf1e5df892578cec6bc26dba md5sum: dacbab0e112d2403b09df138d4e62895
- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams - 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 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 - gatk4/markduplicates
files: files:
- path: output/gatk4/test.bai - path: output/gatk4/test.bai
md5sum: bad71df9c876e72a5bc0a3e0fd755f92 md5sum: 325932c51f6898b02dfec469c984ba28
- path: output/gatk4/test.bam - path: output/gatk4/test.bam
md5sum: d1b85fb578a97f05b484c0d241a9aaad md5sum: f7cba8104e3a7024a5e00c02304f7dea
- path: output/gatk4/test.metrics - path: output/gatk4/test.metrics
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: 6844dc08e677455205e2270ac291c951 md5sum: 14d0d085df7d2f9e770578d92c329299

4
tests/modules/gatk4/splitncigarreads/test.yml
View file

@ -5,6 +5,6 @@
- gatk4/splitncigarreads - gatk4/splitncigarreads
files: files:
- path: output/gatk4/test.bam - path: output/gatk4/test.bam
md5sum: 03068d510523c996814256d9811dc272 md5sum: 1d54057d9f403fba2068ac1aaa4b8a28
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
md5sum: de130e0ab817304404f296b2e512b3b8 md5sum: f0f29af552075dc6bf8a13028e09f8e4