mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
d9e48b70ca
* add software/pairtools * create a branch for pairtools/restrict * fix the different output of conda and docker * remove customized code. * add newline to Frag.bed file. * change the folder of frag.bed. * change \n to \r\n * Remove work.frag.bed Co-authored-by: JoseEspinosa <kadomu@gmail.com>
42 lines
1.4 KiB
Text
42 lines
1.4 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process PAIRTOOLS_RESTRICT {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
publishDir "${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(pairs)
|
|
path frag
|
|
|
|
output:
|
|
tuple val(meta), path("*.pairs.gz"), emit: restrict
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
pairtools \\
|
|
restrict \\
|
|
-f $frag \\
|
|
$options.args \\
|
|
-o ${prefix}.pairs.gz \\
|
|
$pairs
|
|
|
|
echo \$(pairtools --version 2>&1) | sed 's/pairtools.*version //' > ${software}.version.txt
|
|
"""
|
|
}
|