nf-core_modules/software/picard/collectmultiplemetrics/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
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process PICARD_COLLECTMULTIPLEMETRICS {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::picard=2.23.9=0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/picard:2.23.9--0"
} else {
container "quay.io/biocontainers/picard:2.23.9--0"
}
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input:
tuple val(meta), path(bam)
path fasta
output:
tuple val(meta), path("*_metrics"), emit: metrics
tuple val(meta), path("*.pdf") , emit: pdf
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def avail_mem = 3
if (!task.memory) {
log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
picard \\
-Xmx${avail_mem}g \\
CollectMultipleMetrics \\
$options.args \\
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INPUT=$bam \\
OUTPUT=${prefix}.CollectMultipleMetrics \\
REFERENCE_SEQUENCE=$fasta
echo \$(picard CollectMultipleMetrics --version 2>&1) | grep -o 'Version.*' | cut -f2- -d: > ${software}.version.txt
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"""
}