nf-core_modules/software/pairix/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process PAIRIX {
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), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::pairix=0.3.7" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3"
} else {
container "quay.io/biocontainers/pairix:0.3.7--py36h30a8e3e_3"
}
input:
tuple val(meta), path(pair)
output:
tuple val(meta), path(pair), path("*.px2"), emit: index
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
"""
pairix \\
$options.args \\
$pair
echo \$(pairix --help 2>&1) | sed 's/^.*Version: //; s/Usage.*\$//' > ${software}.version.txt
"""
}