nf-core_modules/modules/pairtools/parse/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process PAIRTOOLS_PARSE {
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::pairtools=0.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5"
} else {
container "quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5"
}
input:
tuple val(meta), path(bam)
path chromsizes
output:
tuple val(meta), path("*.pairsam.gz") , emit: pairsam
tuple val(meta), path("*.pairsam.stat"), emit: stat
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
pairtools \\
parse \\
-c $chromsizes \\
$options.args \\
--output-stats ${prefix}.pairsam.stat \\
-o ${prefix}.pairsam.gz \\
$bam
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //')
END_VERSIONS
"""
}