nf-core_modules/software/picard/markduplicates/main.nf
2020-10-12 15:58:09 +01:00

46 lines
1.6 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
process PICARD_MARKDUPLICATES {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
container "quay.io/biocontainers/picard:2.23.6--0"
//container "https://depot.galaxyproject.org/singularity/picard:2.23.6--0"
conda (params.conda ? "bioconda::picard=2.23.6" : null)
input:
tuple val(meta), path(bam)
val options
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 ioptions = initOptions(options)
def prefix = ioptions.suffix ? "${meta.id}${ioptions.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 \\
$ioptions.args \\
INPUT=$bam \\
OUTPUT=${prefix}.bam \\
METRICS_FILE=${prefix}.MarkDuplicates.metrics.txt
echo \$(picard MarkDuplicates --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt
"""
}