mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
Merge pull request #1649 from FriederikeHanssen/gatk_426
update gatk version to 4.2.6.1
This commit is contained in:
FriederikeHanssen
GitHub
commit
0b0556b57f
44 changed files with 133 additions and 150 deletions
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@ -2,10 +2,10 @@ process GATK4_APPLYBQSR {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
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'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
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'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
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@ -2,10 +2,10 @@ process GATK4_APPLYBQSR_SPARK {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
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'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
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'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
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@ -2,10 +2,10 @@ process GATK4_APPLYVQSR {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
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'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
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'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches)
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@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
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'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
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'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(input), path(input_index), path(intervals)
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@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR_SPARK {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
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'broadinstitute/gatk:4.2.3.0' }"
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
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'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(input), path(input_index), path(intervals)
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@ -2,10 +2,10 @@ process GATK4_BEDTOINTERVALLIST {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
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'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
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'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(bed)
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@ -2,10 +2,10 @@ process GATK4_CALCULATECONTAMINATION {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
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'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
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'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(pileup), path(matched)
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@ -2,10 +2,10 @@ process GATK4_COMBINEGVCFS {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
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'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
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'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(vcf), path(vcf_idx)
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@ -2,10 +2,10 @@ process GATK4_CREATESEQUENCEDICTIONARY {
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tag "$fasta"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
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'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
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'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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path fasta
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@ -2,10 +2,10 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
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'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
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'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(genomicsdb)
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@ -2,10 +2,10 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
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'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
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'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(input)
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@ -2,10 +2,10 @@ process GATK4_FASTQTOSAM {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
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'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(reads)
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@ -2,10 +2,10 @@ process GATK4_FILTERMUTECTCALLS {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate)
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@ -2,10 +2,10 @@ process GATK4_GATHERBQSRREPORTS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(table)
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||||
|
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|
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@ -2,10 +2,10 @@ process GATK4_GATHERPILEUPSUMMARIES {
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tag "$meta.id"
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label 'process_low'
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||||
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conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
|
||||
input:
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||||
|
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|
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@ -2,10 +2,10 @@ process GATK4_GENOMICSDBIMPORT {
|
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tag "$meta.id"
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label 'process_low'
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|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace)
|
||||
|
|
|
|||
|
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@ -2,10 +2,10 @@ process GATK4_GENOTYPEGVCFS {
|
|||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_GETPILEUPSUMMARIES {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(index), path(intervals)
|
||||
|
|
@ -40,7 +40,7 @@ process GATK4_GETPILEUPSUMMARIES {
|
|||
--variant $variants \\
|
||||
--output ${prefix}.pileups.table \\
|
||||
$reference_command \\
|
||||
$sites_command \\
|
||||
$interval_command \\
|
||||
--tmp-dir . \\
|
||||
$args
|
||||
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_HAPLOTYPECALLER {
|
|||
tag "$meta.id"
|
||||
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(intervals)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_INDEXFEATUREFILE {
|
|||
tag "$meta.id"
|
||||
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(feature_file)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOBED {
|
|||
tag "$meta.id"
|
||||
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(intervals)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOOLS {
|
|||
tag "$meta.id"
|
||||
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(intervals)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_LEARNREADORIENTATIONMODEL {
|
|||
tag "$meta.id"
|
||||
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(f1r2)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES {
|
|||
tag "$meta.id"
|
||||
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_MERGEBAMALIGNMENT {
|
|||
tag "$meta.id"
|
||||
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(aligned), path(unmapped)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_MERGEMUTECTSTATS {
|
|||
tag "$meta.id"
|
||||
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(stats)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_MERGEVCFS {
|
|||
tag "$meta.id"
|
||||
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_MUTECT2 {
|
|||
tag "$meta.id"
|
||||
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(intervals)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_REVERTSAM {
|
|||
tag "$meta.id"
|
||||
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_SAMTOFASTQ {
|
|||
tag "$meta.id"
|
||||
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_SELECTVARIANTS {
|
|||
tag "$meta.id"
|
||||
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(vcf_idx)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_SPLITNCIGARREADS {
|
|||
tag "$meta.id"
|
||||
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bai), path(intervals)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_VARIANTFILTRATION {
|
|||
tag "$meta.id"
|
||||
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_VARIANTRECALIBRATOR {
|
|||
tag "$meta.id"
|
||||
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 ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi)
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
- gatk4/applybqsr
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: d088422be886dc8507ff97fcc7dd968a
|
||||
md5sum: e11b7eaf2034740a953626518e3c3d6e
|
||||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 applybqsr test_gatk4_applybqsr_intervals
|
||||
|
|
@ -15,7 +15,7 @@
|
|||
- gatk4/applybqsr
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 4bfa18d651abd945e240b05e70107716
|
||||
md5sum: e9e9aa753c106e43f936ad573e23d2e6
|
||||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 applybqsr test_gatk4_applybqsr_cram
|
||||
|
|
@ -25,5 +25,5 @@
|
|||
- gatk4/applybqsr
|
||||
files:
|
||||
- path: output/gatk4/test.cram
|
||||
md5sum: 2e0bca197af4f043a4a85152e6edbe04
|
||||
md5sum: bca9d234a5d484ce2a6f4826ca2ea308
|
||||
- path: output/gatk4/versions.yml
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
- gatk4/applybqsrspark
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: d088422be886dc8507ff97fcc7dd968a
|
||||
md5sum: 1901c819fcba0fdd5e2482e6dc8285ef
|
||||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 applybqsr test_gatk4_applybqsr_spark_intervals
|
||||
|
|
@ -15,7 +15,7 @@
|
|||
- gatk4/applybqsrspark
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 4bfa18d651abd945e240b05e70107716
|
||||
md5sum: 2ca2446f0125890280056fd7da822732
|
||||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 applybqsr test_gatk4_applybqsr_spark_cram
|
||||
|
|
@ -25,5 +25,5 @@
|
|||
- gatk4/applybqsrspark
|
||||
files:
|
||||
- path: output/gatk4/test.cram
|
||||
md5sum: 2e0bca197af4f043a4a85152e6edbe04
|
||||
md5sum: 60f7c822a9f2833e11eb7bfd16e4421f
|
||||
- path: output/gatk4/versions.yml
|
||||
|
|
|
|||
|
|
@ -1,6 +1,5 @@
|
|||
process {
|
||||
|
||||
ext.args = "--tmp-dir ."
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
|
|
@ -65,7 +65,9 @@ workflow test_gatk4_genotypegvcfs_gz_input_intervals {
|
|||
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_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)
|
||||
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
|
||||
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']['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)
|
||||
|
|
@ -106,6 +109,7 @@ workflow test_gatk4_genotypegvcfs_gendb_input {
|
|||
gendb = UNTAR.out.untar.map{ it[1] }.collect()
|
||||
gendb.add([])
|
||||
gendb.add([])
|
||||
gendb.add([])
|
||||
|
||||
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.add([])
|
||||
gendb.add([])
|
||||
gendb.add([])
|
||||
input = Channel.of([ id:'test' ]).combine(gendb)
|
||||
|
||||
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.add([])
|
||||
gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
|
||||
gendb.add([])
|
||||
|
||||
input = Channel.of([ id:'test' ]).combine(gendb)
|
||||
|
||||
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.add([])
|
||||
gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
|
||||
gendb.add([])
|
||||
|
||||
input = Channel.of([ id:'test' ]).combine(gendb)
|
||||
|
||||
GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi )
|
||||
|
|
|
|||
|
|
@ -4,21 +4,6 @@ nextflow.enable.dsl = 2
|
|||
|
||||
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 {
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c tests/config/nextflow.config
|
||||
tags:
|
||||
|
|
|
|||
|
|
@ -7,11 +7,11 @@
|
|||
- path: output/gatk4/test.interval_list
|
||||
md5sum: e51101c9357fb2d59fd30e370eefa39c
|
||||
- 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
|
||||
md5sum: 0728d164666d9264ef442a493e008dee
|
||||
md5sum: 59f1978c5f4ef3fce3b110816283d9f5
|
||||
- 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
|
||||
md5sum: d29ca4447f32547f2936567fa902796a
|
||||
md5sum: c24044490cfedbcba61dbc646d3aa570
|
||||
- path: output/gatk4/versions.yml
|
||||
|
|
|
|||
|
|
@ -5,9 +5,9 @@
|
|||
- gatk4/markduplicates
|
||||
files:
|
||||
- path: output/gatk4/test.bai
|
||||
md5sum: e9c125e82553209933883b4fe2b8d7c2
|
||||
md5sum: c8f7a9e426c768577f88f59cb1336bf3
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 2efd50b2e6b7fd9bdf242cd9e266cfa9
|
||||
md5sum: 58533ddab47f7ac07f7b10e7f4aac234
|
||||
- path: output/gatk4/test.metrics
|
||||
- path: output/gatk4/versions.yml
|
||||
|
||||
|
|
@ -20,6 +20,6 @@
|
|||
- path: output/gatk4/test.bai
|
||||
md5sum: bad71df9c876e72a5bc0a3e0fd755f92
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 8187febc6108ffef7f907e89b9c091a4
|
||||
md5sum: 112580c24b43331950f24f9adea30788
|
||||
- path: output/gatk4/test.metrics
|
||||
- path: output/gatk4/versions.yml
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
- gatk4/splitncigarreads
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 436d8e31285c6b588bdd1c7f1d07f6f2
|
||||
md5sum: 37e5dbce8692b54c3292b539c91dfbd7
|
||||
- path: output/gatk4/versions.yml
|
||||
- name: gatk4 splitncigarreads test_gatk4_splitncigarreads_intervals
|
||||
command: nextflow run tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads_intervals -c tests/config/nextflow.config
|
||||
|
|
@ -14,5 +14,5 @@
|
|||
- gatk4/splitncigarreads
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: cd56e3225950f519fd47164cca60a0bb
|
||||
md5sum: e5cd2fd1822298a9bf7bc8b8d42146af
|
||||
- path: output/gatk4/versions.yml
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@
|
|||
- "#CHROM POS ID REF ALT QUAL FILTER INFO"
|
||||
- path: output/gatk4/test.recal.idx
|
||||
- path: output/gatk4/test.tranches
|
||||
md5sum: d238e97bf996863969dac7751e345549
|
||||
md5sum: c029e52fd63a893e1154cc9144a19eeb
|
||||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 variantrecalibrator test_gatk4_variantrecalibrator_allele_specific
|
||||
|
|
@ -23,5 +23,5 @@
|
|||
- "#CHROM POS ID REF ALT QUAL FILTER INFO"
|
||||
- path: output/gatk4/test.recal.idx
|
||||
- path: output/gatk4/test.tranches
|
||||
md5sum: 444438d46716593634a6817958099292
|
||||
md5sum: ad52fa69325c758f458a30ee5b43d6b5
|
||||
- path: output/gatk4/versions.yml
|
||||
|
|
|
|||
Loading…
Reference in a new issue