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Bump picard version from 2.25.7 to 2.26.7 for log4j vulnerability (#1173)

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* Bump picard version from 2.25.7 to 2.26.7 for log4j vulnerability

* Fix EC lint for unrelated hmmcopy module
This commit is contained in:
Harshil Patel 2021-12-16 10:56:41 +00:00 committed by GitHub
parent 54e0ac4ed9
commit 0d1e21686a
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GPG key ID: 4AEE18F83AFDEB23
7 changed files with 21 additions and 21 deletions
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6
modules/picard/collecthsmetrics/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.2" : null)
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.2--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.2--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

6
modules/picard/collectmultiplemetrics/main.nf
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@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

6
modules/picard/collectwgsmetrics/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_COLLECTWGSMETRICS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
input:
tuple val(meta), path(bam), path(bai)

6
modules/picard/filtersamreads/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
input:
tuple val(meta), path(bam), path(readlist)

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

@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

6
modules/picard/mergesamfiles/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
input:
tuple val(meta), path(bams)

6
modules/picard/sortsam/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_SORTSAM {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
input:
tuple val(meta), path(bam)