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Update picard version command and default container

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This commit is contained in:
drpatelh 2020-10-19 15:17:19 +01:00
parent ff0fe1a910
commit 47d390772c
3 changed files with 13 additions and 13 deletions
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8
software/picard/collectmultiplemetrics/main.nf
View file

@ -11,11 +11,11 @@ process PICARD_COLLECTMULTIPLEMETRICS {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } 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) { 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 { } else {
container "quay.io/biocontainers/picard:2.23.6--0" container "quay.io/biocontainers/picard:2.23.8--0"
} }
input: input:
@ -45,6 +45,6 @@ process PICARD_COLLECTMULTIPLEMETRICS {
OUTPUT=${prefix}.CollectMultipleMetrics \\ OUTPUT=${prefix}.CollectMultipleMetrics \\
REFERENCE_SEQUENCE=$fasta REFERENCE_SEQUENCE=$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
""" """
} }

8
software/picard/markduplicates/main.nf
View file

@ -11,11 +11,11 @@ process PICARD_MARKDUPLICATES {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } 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) { 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 { } else {
container "quay.io/biocontainers/picard:2.23.6--0" container "quay.io/biocontainers/picard:2.23.8--0"
} }
input: input:
@ -44,6 +44,6 @@ process PICARD_MARKDUPLICATES {
OUTPUT=${prefix}.bam \\ OUTPUT=${prefix}.bam \\
METRICS_FILE=${prefix}.MarkDuplicates.metrics.txt METRICS_FILE=${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
""" """
} }

10
software/picard/mergesamfiles/main.nf
View file

@ -11,11 +11,11 @@ process PICARD_MERGESAMFILES {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } 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) { 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 { } else {
container "quay.io/biocontainers/picard:2.23.6--0" container "quay.io/biocontainers/picard:2.23.8--0"
} }
input: input:
@ -43,12 +43,12 @@ process PICARD_MERGESAMFILES {
$options.args \\ $options.args \\
${'INPUT='+bam_files.join(' INPUT=')} \\ ${'INPUT='+bam_files.join(' INPUT=')} \\
OUTPUT=${prefix}.bam 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 { } else {
""" """
ln -s ${bam_files[0]} ${prefix}.bam 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
""" """
} }
} }