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update gatk version

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This commit is contained in:
Rike 2022-05-12 15:45:21 +02:00
parent 2061a41803
commit 169b2b96c1
33 changed files with 99 additions and 99 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
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@ -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/bedtointervallist/main.nf
View file

@ -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
View file

@ -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
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@ -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)

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=4.2.5.0" : 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)

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)