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Merge pull request #1649 from FriederikeHanssen/gatk_426

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update gatk version to 4.2.6.1
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FriederikeHanssen 2022-05-16 11:24:14 +02:00 committed by GitHub
commit 0b0556b57f
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44 changed files with 133 additions and 150 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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--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/applybqsrspark/main.nf
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@ -2,10 +2,10 @@ process GATK4_APPLYBQSR_SPARK {
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=4.2.6.1" : 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/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches) tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), 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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--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/baserecalibratorspark/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR_SPARK {
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=4.2.6.1" : 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/gatk4:4.2.6.1--hdfd78af_0':
'broadinstitute/gatk:4.2.3.0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(pileup), path(matched) tuple val(meta), path(pileup), path(matched)

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

@ -2,10 +2,10 @@ process GATK4_COMBINEGVCFS {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(vcf), path(vcf_idx) tuple val(meta), path(vcf), path(vcf_idx)

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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
path fasta path fasta

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

@ -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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(genomicsdb) tuple val(meta), path(genomicsdb)

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

@ -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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(input) tuple val(meta), path(input)

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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate) tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate)

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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(table) tuple val(meta), path(table)

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

@ -2,10 +2,10 @@ process GATK4_GATHERPILEUPSUMMARIES {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:

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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace) tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), 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_high' label 'process_high'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index) tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index)

8
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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(input), path(index), path(intervals) tuple val(meta), path(input), path(index), path(intervals)
@ -40,7 +40,7 @@ process GATK4_GETPILEUPSUMMARIES {
--variant $variants \\ --variant $variants \\
--output ${prefix}.pileups.table \\ --output ${prefix}.pileups.table \\
$reference_command \\ $reference_command \\
$sites_command \\ $interval_command \\
--tmp-dir . \\ --tmp-dir . \\
$args $args

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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(feature_file) tuple val(meta), path(feature_file)

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

@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOBED {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(intervals) tuple val(meta), path(intervals)

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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(intervals) tuple val(meta), path(intervals)

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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(aligned), path(unmapped) tuple val(meta), path(aligned), path(unmapped)

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

@ -2,10 +2,10 @@ process GATK4_MERGEMUTECTSTATS {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(stats) tuple val(meta), path(stats)

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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(vcf) tuple val(meta), path(vcf)

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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--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/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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

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

@ -2,10 +2,10 @@ process GATK4_SELECTVARIANTS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0': 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(vcf), path(vcf_idx) tuple val(meta), path(vcf), path(vcf_idx)

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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam), path(bai), path(intervals) tuple val(meta), path(bam), path(bai), path(intervals)

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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(vcf), path(tbi) tuple val(meta), path(vcf), path(tbi)

6
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=4.2.5.0" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : 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/gatk4:4.2.5.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(vcf), path(tbi) tuple val(meta), path(vcf), path(tbi)

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

@ -5,7 +5,7 @@
- gatk4/applybqsr - gatk4/applybqsr
files: files:
- path: output/gatk4/test.bam - path: output/gatk4/test.bam
md5sum: d088422be886dc8507ff97fcc7dd968a md5sum: e11b7eaf2034740a953626518e3c3d6e
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
- name: gatk4 applybqsr test_gatk4_applybqsr_intervals - name: gatk4 applybqsr test_gatk4_applybqsr_intervals
@ -15,7 +15,7 @@
- gatk4/applybqsr - gatk4/applybqsr
files: files:
- path: output/gatk4/test.bam - path: output/gatk4/test.bam
md5sum: 4bfa18d651abd945e240b05e70107716 md5sum: e9e9aa753c106e43f936ad573e23d2e6
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
- name: gatk4 applybqsr test_gatk4_applybqsr_cram - name: gatk4 applybqsr test_gatk4_applybqsr_cram
@ -25,5 +25,5 @@
- gatk4/applybqsr - gatk4/applybqsr
files: files:
- path: output/gatk4/test.cram - path: output/gatk4/test.cram
md5sum: 2e0bca197af4f043a4a85152e6edbe04 md5sum: bca9d234a5d484ce2a6f4826ca2ea308
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml

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

@ -5,7 +5,7 @@
- gatk4/applybqsrspark - gatk4/applybqsrspark
files: files:
- path: output/gatk4/test.bam - path: output/gatk4/test.bam
md5sum: d088422be886dc8507ff97fcc7dd968a md5sum: 1901c819fcba0fdd5e2482e6dc8285ef
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
- name: gatk4 applybqsr test_gatk4_applybqsr_spark_intervals - name: gatk4 applybqsr test_gatk4_applybqsr_spark_intervals
@ -15,7 +15,7 @@
- gatk4/applybqsrspark - gatk4/applybqsrspark
files: files:
- path: output/gatk4/test.bam - path: output/gatk4/test.bam
md5sum: 4bfa18d651abd945e240b05e70107716 md5sum: 2ca2446f0125890280056fd7da822732
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
- name: gatk4 applybqsr test_gatk4_applybqsr_spark_cram - name: gatk4 applybqsr test_gatk4_applybqsr_spark_cram
@ -25,5 +25,5 @@
- gatk4/applybqsrspark - gatk4/applybqsrspark
files: files:
- path: output/gatk4/test.cram - path: output/gatk4/test.cram
md5sum: 2e0bca197af4f043a4a85152e6edbe04 md5sum: 60f7c822a9f2833e11eb7bfd16e4421f
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml

1
tests/modules/gatk4/combinegvcfs/nextflow.config
View file

@ -1,6 +1,5 @@
process { process {
ext.args = "--tmp-dir ."
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
} }

13
tests/modules/gatk4/genotypegvcfs/main.nf
View file

@ -65,7 +65,9 @@ workflow test_gatk4_genotypegvcfs_gz_input_intervals {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ] file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ,
[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) 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) fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
@ -80,7 +82,8 @@ workflow test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
[]
] ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
@ -106,6 +109,7 @@ workflow test_gatk4_genotypegvcfs_gendb_input {
gendb = UNTAR.out.untar.map{ it[1] }.collect() gendb = UNTAR.out.untar.map{ it[1] }.collect()
gendb.add([]) gendb.add([])
gendb.add([]) gendb.add([])
gendb.add([])
input = Channel.of([ id:'test' ]).combine(gendb) input = Channel.of([ id:'test' ]).combine(gendb)
@ -128,6 +132,7 @@ workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp {
gendb = UNTAR.out.untar.map{ it[1] }.collect() gendb = UNTAR.out.untar.map{ it[1] }.collect()
gendb.add([]) gendb.add([])
gendb.add([]) gendb.add([])
gendb.add([])
input = Channel.of([ id:'test' ]).combine(gendb) input = Channel.of([ id:'test' ]).combine(gendb)
GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi) GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi)
@ -146,6 +151,8 @@ workflow test_gatk4_genotypegvcfs_gendb_input_intervals {
gendb = UNTAR.out.untar.map{ it[1] }.collect() gendb = UNTAR.out.untar.map{ it[1] }.collect()
gendb.add([]) gendb.add([])
gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)]) gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
gendb.add([])
input = Channel.of([ id:'test' ]).combine(gendb) input = Channel.of([ id:'test' ]).combine(gendb)
GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [] ) GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [] )
@ -167,6 +174,8 @@ workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals {
gendb = UNTAR.out.untar.map{ it[1] }.collect() gendb = UNTAR.out.untar.map{ it[1] }.collect()
gendb.add([]) gendb.add([])
gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)]) gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
gendb.add([])
input = Channel.of([ id:'test' ]).combine(gendb) input = Channel.of([ id:'test' ]).combine(gendb)
GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi ) GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi )

15
tests/modules/gatk4/getpileupsummaries/main.nf
View file

@ -4,21 +4,6 @@ nextflow.enable.dsl = 2
include { GATK4_GETPILEUPSUMMARIES } from '../../../../modules/gatk4/getpileupsummaries/main.nf' include { GATK4_GETPILEUPSUMMARIES } from '../../../../modules/gatk4/getpileupsummaries/main.nf'
workflow test_gatk4_getpileupsummaries_just_variants {
input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) ,
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
[]
]
variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
fasta = []
fai = []
dict = []
GATK4_GETPILEUPSUMMARIES ( input , fasta, fai, dict, variants , variants_tbi )
}
workflow test_gatk4_getpileupsummaries_separate_sites { workflow test_gatk4_getpileupsummaries_separate_sites {

10
tests/modules/gatk4/getpileupsummaries/test.yml
View file

@ -1,13 +1,3 @@
- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_just_variants
command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_just_variants -c tests/config/nextflow.config
tags:
- gatk4/getpileupsummaries
- gatk4
files:
- path: output/gatk4/test.pileups.table
md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
- path: output/gatk4/versions.yml
- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites - 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 command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c tests/config/nextflow.config
tags: tags:

8
tests/modules/gatk4/intervallisttools/test.yml
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@ -7,11 +7,11 @@
- path: output/gatk4/test.interval_list - path: output/gatk4/test.interval_list
md5sum: e51101c9357fb2d59fd30e370eefa39c md5sum: e51101c9357fb2d59fd30e370eefa39c
- path: output/gatk4/test_split/temp_0001_of_6/1scattered.interval_list - path: output/gatk4/test_split/temp_0001_of_6/1scattered.interval_list
md5sum: b8ba8a387200df76a0d1c577626dc265 md5sum: 39385d38ac6cb7c05190026fc3b81411
- path: output/gatk4/test_split/temp_0002_of_6/2scattered.interval_list - path: output/gatk4/test_split/temp_0002_of_6/2scattered.interval_list
md5sum: 0728d164666d9264ef442a493e008dee md5sum: 59f1978c5f4ef3fce3b110816283d9f5
- path: output/gatk4/test_split/temp_0003_of_6/3scattered.interval_list - path: output/gatk4/test_split/temp_0003_of_6/3scattered.interval_list
md5sum: 55da0f3c69504148f4e7002a0e072cfe md5sum: 709fe81bfcf700bd80d96c62a71629fd
- path: output/gatk4/test_split/temp_0004_of_6/4scattered.interval_list - path: output/gatk4/test_split/temp_0004_of_6/4scattered.interval_list
md5sum: d29ca4447f32547f2936567fa902796a md5sum: c24044490cfedbcba61dbc646d3aa570
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml

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

@ -5,9 +5,9 @@
- 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: 2efd50b2e6b7fd9bdf242cd9e266cfa9 md5sum: 58533ddab47f7ac07f7b10e7f4aac234
- path: output/gatk4/test.metrics - path: output/gatk4/test.metrics
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
@ -20,6 +20,6 @@
- path: output/gatk4/test.bai - path: output/gatk4/test.bai
md5sum: bad71df9c876e72a5bc0a3e0fd755f92 md5sum: bad71df9c876e72a5bc0a3e0fd755f92
- path: output/gatk4/test.bam - path: output/gatk4/test.bam
md5sum: 8187febc6108ffef7f907e89b9c091a4 md5sum: 112580c24b43331950f24f9adea30788
- path: output/gatk4/test.metrics - path: output/gatk4/test.metrics
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml

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

@ -5,7 +5,7 @@
- gatk4/splitncigarreads - gatk4/splitncigarreads
files: files:
- path: output/gatk4/test.bam - path: output/gatk4/test.bam
md5sum: 436d8e31285c6b588bdd1c7f1d07f6f2 md5sum: 37e5dbce8692b54c3292b539c91dfbd7
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
- name: gatk4 splitncigarreads test_gatk4_splitncigarreads_intervals - name: gatk4 splitncigarreads test_gatk4_splitncigarreads_intervals
command: nextflow run tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads_intervals -c tests/config/nextflow.config command: nextflow run tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads_intervals -c tests/config/nextflow.config
@ -14,5 +14,5 @@
- gatk4/splitncigarreads - gatk4/splitncigarreads
files: files:
- path: output/gatk4/test.bam - path: output/gatk4/test.bam
md5sum: cd56e3225950f519fd47164cca60a0bb md5sum: e5cd2fd1822298a9bf7bc8b8d42146af
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml

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

@ -9,7 +9,7 @@
- "#CHROM POS ID REF ALT QUAL FILTER INFO" - "#CHROM POS ID REF ALT QUAL FILTER INFO"
- path: output/gatk4/test.recal.idx - path: output/gatk4/test.recal.idx
- path: output/gatk4/test.tranches - path: output/gatk4/test.tranches
md5sum: d238e97bf996863969dac7751e345549 md5sum: c029e52fd63a893e1154cc9144a19eeb
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
- name: gatk4 variantrecalibrator test_gatk4_variantrecalibrator_allele_specific - name: gatk4 variantrecalibrator test_gatk4_variantrecalibrator_allele_specific
@ -23,5 +23,5 @@
- "#CHROM POS ID REF ALT QUAL FILTER INFO" - "#CHROM POS ID REF ALT QUAL FILTER INFO"
- path: output/gatk4/test.recal.idx - path: output/gatk4/test.recal.idx
- path: output/gatk4/test.tranches - path: output/gatk4/test.tranches
md5sum: 444438d46716593634a6817958099292 md5sum: ad52fa69325c758f458a30ee5b43d6b5
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml