mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 21:53:10 +00:00
8d4c6de50d
* add software/cooler * fix the wrong files uploaded. * create a branch for cooler/dump * remove the bin size from metadata.
39 lines
1.3 KiB
Text
39 lines
1.3 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process COOLER_DUMP {
|
|
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::cooler=0.8.11" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0"
|
|
} else {
|
|
container "quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(cool)
|
|
|
|
output:
|
|
tuple val(meta), path("*.bedpe"), emit: bedpe
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
cooler dump \\
|
|
$options.args \\
|
|
-o ${prefix}.bedpe \\
|
|
$cool
|
|
|
|
echo \$(cooler --version 2>&1) | sed 's/cooler, version //' > ${software}.version.txt
|
|
"""
|
|
}
|