nf-core_modules/modules/fgbio/fastqtobam/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process FGBIO_FASTQTOBAM {
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), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::fgbio=1.4.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/fgbio:1.4.0--hdfd78af_0"
} else {
container "quay.io/biocontainers/fgbio:1.4.0--hdfd78af_0"
}
input:
tuple val(meta), path(reads)
val(read_structure)
output:
tuple val(meta), path("*_umi_converted.bam"), emit: umibam
path "versions.yml" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
mkdir tmpFolder
fgbio \\
--tmp-dir=${PWD}/tmpFolder \\
FastqToBam \\
-i $reads \\
-o "${prefix}_umi_converted.bam" \\
--read-structures $read_structure \\
--sample $meta.id \\
--library $meta.id \\
$options.args
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//')
END_VERSIONS
"""
}