mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
4e5b6ed843
* Fix picard/markduplicates with new options syntax * Delete md5sum for bam files and add contains for metrics.txt Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
52 lines
1.9 KiB
Text
52 lines
1.9 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process PICARD_MARKDUPLICATES {
|
|
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(bam)
|
|
|
|
output:
|
|
tuple val(meta), path("*.bam") , emit: bam
|
|
tuple val(meta), path("*.bai") , optional:true, emit: bai
|
|
tuple val(meta), path("*.metrics.txt"), emit: metrics
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def avail_mem = 3
|
|
if (!task.memory) {
|
|
log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
|
} else {
|
|
avail_mem = task.memory.giga
|
|
}
|
|
"""
|
|
picard \\
|
|
-Xmx${avail_mem}g \\
|
|
MarkDuplicates \\
|
|
$options.args \\
|
|
I=$bam \\
|
|
O=${prefix}.bam \\
|
|
M=${prefix}.MarkDuplicates.metrics.txt
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
|
|
END_VERSIONS
|
|
"""
|
|
}
|