mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
0d1e21686a
* Bump picard version from 2.25.7 to 2.26.7 for log4j vulnerability * Fix EC lint for unrelated hmmcopy module
42 lines
1.4 KiB
Text
42 lines
1.4 KiB
Text
process PICARD_COLLECTMULTIPLEMETRICS {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
|
|
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(bam)
|
|
path fasta
|
|
|
|
output:
|
|
tuple val(meta), path("*_metrics"), emit: metrics
|
|
tuple val(meta), path("*.pdf") , emit: pdf
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def avail_mem = 3
|
|
if (!task.memory) {
|
|
log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
|
} else {
|
|
avail_mem = task.memory.giga
|
|
}
|
|
"""
|
|
picard \\
|
|
-Xmx${avail_mem}g \\
|
|
CollectMultipleMetrics \\
|
|
$args \\
|
|
INPUT=$bam \\
|
|
OUTPUT=${prefix}.CollectMultipleMetrics \\
|
|
REFERENCE_SEQUENCE=$fasta
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
picard: \$(picard CollectMultipleMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
|
|
END_VERSIONS
|
|
"""
|
|
}
|