nf-core_modules/modules/picard/markduplicates/main.nf

50 lines
1.7 KiB
Text
Raw Normal View History

2020-09-10 15:45:11 +00:00
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
2020-09-10 15:45:11 +00:00
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']) }
2020-12-17 23:50:24 +00:00
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"
}
2020-09-10 15:45:11 +00:00
input:
tuple val(meta), path(bam)
2020-12-17 23:50:24 +00:00
2020-09-10 15:45:11 +00:00
output:
tuple val(meta), path("*.bam") , emit: bam
tuple val(meta), path("*.metrics.txt"), emit: metrics
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
2020-09-10 15:45:11 +00:00
def avail_mem = 3
if (!task.memory) {
log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
picard \\
-Xmx${avail_mem}g \\
MarkDuplicates \\
$options.args \\
2020-09-10 15:45:11 +00:00
INPUT=$bam \\
OUTPUT=${prefix}.bam \\
METRICS_FILE=${prefix}.MarkDuplicates.metrics.txt
echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt
2020-09-10 15:45:11 +00:00
"""
}