nf-core_modules/software/gatk4/mergebamalignment/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process GATK4_MERGEBAMALIGNMENT {
tag "$meta.id"
label 'process_low'
publishDir "${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::gatk4=4.2.0.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
}
input:
tuple val(meta), path(aligned)
path unmapped
path fasta
path dict
output:
tuple val(meta), path('*.merged.bam'), emit: bam
path '*.version.txt' , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
"""
gatk MergeBamAlignment \\
ALIGNED=$aligned \\
UNMAPPED=$unmapped \\
R=$fasta \\
O=${prefix}.merged.bam \\
$options.args
gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
"""
}