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

43 lines
1.4 KiB
Text
Raw Normal View History

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process PAIRTOOLS_FLIP {
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(sam)
path chromsizes
output:
tuple val(meta), path("*.flip.gz"), emit: flip
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
pairtools \\
flip \\
-c $chromsizes \\
$options.args \\
-o ${prefix}.flip.gz \\
$sam
echo \$(pairtools --version 2>&1) | sed 's/pairtools.*version //' > ${software}.version.txt
"""
}