From 0d1e21686a586447b7592e40da9b3a7cdeedf03c Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 16 Dec 2021 10:56:41 +0000 Subject: [PATCH] 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 --- modules/picard/collecthsmetrics/main.nf | 6 +++--- modules/picard/collectmultiplemetrics/main.nf | 6 +++--- modules/picard/collectwgsmetrics/main.nf | 6 +++--- modules/picard/filtersamreads/main.nf | 6 +++--- modules/picard/markduplicates/main.nf | 6 +++--- modules/picard/mergesamfiles/main.nf | 6 +++--- modules/picard/sortsam/main.nf | 6 +++--- 7 files changed, 21 insertions(+), 21 deletions(-) diff --git a/modules/picard/collecthsmetrics/main.nf b/modules/picard/collecthsmetrics/main.nf index 3705b8fb..9dabc3aa 100644 --- a/modules/picard/collecthsmetrics/main.nf +++ b/modules/picard/collecthsmetrics/main.nf @@ -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) diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf index 6b292534..481761e3 100644 --- a/modules/picard/collectmultiplemetrics/main.nf +++ b/modules/picard/collectmultiplemetrics/main.nf @@ -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) diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf index eddb4604..361ca1b5 100644 --- a/modules/picard/collectwgsmetrics/main.nf +++ b/modules/picard/collectwgsmetrics/main.nf @@ -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) diff --git a/modules/picard/filtersamreads/main.nf b/modules/picard/filtersamreads/main.nf index d8de137b..70bd2fa7 100644 --- a/modules/picard/filtersamreads/main.nf +++ b/modules/picard/filtersamreads/main.nf @@ -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) diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf index d3bf6938..3087bff4 100644 --- a/modules/picard/markduplicates/main.nf +++ b/modules/picard/markduplicates/main.nf @@ -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) diff --git a/modules/picard/mergesamfiles/main.nf b/modules/picard/mergesamfiles/main.nf index 86796593..952d6331 100644 --- a/modules/picard/mergesamfiles/main.nf +++ b/modules/picard/mergesamfiles/main.nf @@ -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) diff --git a/modules/picard/sortsam/main.nf b/modules/picard/sortsam/main.nf index eb3caf40..7728484c 100644 --- a/modules/picard/sortsam/main.nf +++ b/modules/picard/sortsam/main.nf @@ -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)