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

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2021-02-19 11:41:29 +00:00
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process GATK4_SAMTOFASTQ {
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), publish_id:meta.id) }
conda (params.enable_conda ? 'bioconda::gatk4:4.1.9.0' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0'
} else {
container 'quay.io/biocontainers/gatk4:4.1.9.0--py39_0'
}
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path('*.fastq.gz') , emit: fastq
path '*.version.txt' , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
def output = meta.single_end ? "FASTQ=${prefix}.fastq.gz" : "FASTQ=${prefix}_1.fastq.gz SECOND_END_FASTQ=${prefix}_2.fastq.gz"
"""
gatk SamToFastq \\
I=$bam \\
$output \\
$options.args
gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
"""
}