mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
40 lines
1.2 KiB
Text
40 lines
1.2 KiB
Text
process COOLER_CLOAD {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
|
|
conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
|
|
'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(pairs), path(index)
|
|
val cool_bin
|
|
path chromsizes
|
|
|
|
output:
|
|
tuple val(meta), val(cool_bin), path("*.cool"), emit: cool
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def nproc = args.contains('pairix') || args.contains('tabix')? "--nproc $task.cpus" : ''
|
|
|
|
"""
|
|
cooler cload \\
|
|
$args \\
|
|
$nproc \\
|
|
${chromsizes}:${cool_bin} \\
|
|
$pairs \\
|
|
${prefix}.${cool_bin}.cool
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
cooler: \$(cooler --version 2>&1 | sed 's/cooler, version //')
|
|
END_VERSIONS
|
|
"""
|
|
}
|