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Bump picard version from 2.25.7 to 2.26.7 for log4j vulnerability (#1173)
* Bump picard version from 2.25.7 to 2.26.7 for log4j vulnerability * Fix EC lint for unrelated hmmcopy module
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7 changed files with 21 additions and 21 deletions
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@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::picard=2.26.2" : null)
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conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/picard:2.26.2--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.26.2--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
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input:
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tuple val(meta), path(bam)
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@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
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conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
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input:
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tuple val(meta), path(bam)
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@ -2,10 +2,10 @@ process PICARD_COLLECTWGSMETRICS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
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conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
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input:
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tuple val(meta), path(bam), path(bai)
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@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
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conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
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input:
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tuple val(meta), path(bam), path(readlist)
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@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
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conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
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input:
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tuple val(meta), path(bam)
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@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
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conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
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input:
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tuple val(meta), path(bams)
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@ -2,10 +2,10 @@ process PICARD_SORTSAM {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
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conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
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input:
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tuple val(meta), path(bam)
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