From 47d390772c6d977d86f7b64f1d50045e8dc75c59 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Mon, 19 Oct 2020 15:17:19 +0100 Subject: [PATCH] Update picard version command and default container --- software/picard/collectmultiplemetrics/main.nf | 8 ++++---- software/picard/markduplicates/main.nf | 8 ++++---- software/picard/mergesamfiles/main.nf | 10 +++++----- 3 files changed, 13 insertions(+), 13 deletions(-) diff --git a/software/picard/collectmultiplemetrics/main.nf b/software/picard/collectmultiplemetrics/main.nf index ff0c0835..b9f8e496 100644 --- a/software/picard/collectmultiplemetrics/main.nf +++ b/software/picard/collectmultiplemetrics/main.nf @@ -11,11 +11,11 @@ process PICARD_COLLECTMULTIPLEMETRICS { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::picard=2.23.6" : null) + conda (params.enable_conda ? "bioconda::picard=2.23.8" : null) if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0" + container "https://depot.galaxyproject.org/singularity/picard:2.23.8--0" } else { - container "quay.io/biocontainers/picard:2.23.6--0" + container "quay.io/biocontainers/picard:2.23.8--0" } input: @@ -45,6 +45,6 @@ process PICARD_COLLECTMULTIPLEMETRICS { OUTPUT=${prefix}.CollectMultipleMetrics \\ REFERENCE_SEQUENCE=$fasta - echo \$(picard CollectMultipleMetrics --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt + echo \$(picard CollectMultipleMetrics --version 2>&1) | grep -o 'Version.*' | cut -f2- -d: > ${software}.version.txt """ } diff --git a/software/picard/markduplicates/main.nf b/software/picard/markduplicates/main.nf index 924f8a94..94c46b82 100644 --- a/software/picard/markduplicates/main.nf +++ b/software/picard/markduplicates/main.nf @@ -11,11 +11,11 @@ process PICARD_MARKDUPLICATES { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::picard=2.23.6" : null) + conda (params.enable_conda ? "bioconda::picard=2.23.8" : null) if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0" + container "https://depot.galaxyproject.org/singularity/picard:2.23.8--0" } else { - container "quay.io/biocontainers/picard:2.23.6--0" + container "quay.io/biocontainers/picard:2.23.8--0" } input: @@ -44,6 +44,6 @@ process PICARD_MARKDUPLICATES { OUTPUT=${prefix}.bam \\ METRICS_FILE=${prefix}.MarkDuplicates.metrics.txt - echo \$(picard MarkDuplicates --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt + echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt """ } diff --git a/software/picard/mergesamfiles/main.nf b/software/picard/mergesamfiles/main.nf index 295cc259..09c36ebf 100644 --- a/software/picard/mergesamfiles/main.nf +++ b/software/picard/mergesamfiles/main.nf @@ -11,11 +11,11 @@ process PICARD_MERGESAMFILES { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::picard=2.23.6" : null) + conda (params.enable_conda ? "bioconda::picard=2.23.8" : null) if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0" + container "https://depot.galaxyproject.org/singularity/picard:2.23.8--0" } else { - container "quay.io/biocontainers/picard:2.23.6--0" + container "quay.io/biocontainers/picard:2.23.8--0" } input: @@ -43,12 +43,12 @@ process PICARD_MERGESAMFILES { $options.args \\ ${'INPUT='+bam_files.join(' INPUT=')} \\ OUTPUT=${prefix}.bam - echo \$(picard MergeSamFiles --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt + echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt """ } else { """ ln -s ${bam_files[0]} ${prefix}.bam - echo \$(picard MergeSamFiles --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt + echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt """ } }