nf-core_modules/software/picard/mergesamfiles/main.nf
2020-12-17 17:50:24 -06:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process PICARD_MERGESAMFILES {
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) }
conda (params.enable_conda ? "bioconda::picard=2.23.9" : null)
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"
}
input:
tuple val(meta), path(bams)
output:
tuple val(meta), path("*.bam"), emit: bam
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def bam_files = bams.sort()
def avail_mem = 3
if (!task.memory) {
log.info '[Picard MergeSamFiles] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
if (bam_files.size() > 1) {
"""
picard \\
-Xmx${avail_mem}g \\
MergeSamFiles \\
$options.args \\
${'INPUT='+bam_files.join(' INPUT=')} \\
OUTPUT=${prefix}.bam
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) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt
"""
}
}