nf-core_modules/modules/picard/mergesamfiles/main.nf
Harshil Patel 7b3315591a
Remove def software lines and emit versions channel as plural (#780)
* Remove def software line

* Replace version with versions in emit statement

* Fix default software names
2021-10-01 14:04:56 +01:00

59 lines
2.1 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
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), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
} else {
container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
}
input:
tuple val(meta), path(bams)
output:
tuple val(meta), path("*.bam"), emit: bam
path "versions.yml" , emit: versions
script:
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
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
} else {
"""
ln -s ${bam_files[0]} ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
}
}