mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
39 lines
1.3 KiB
Text
39 lines
1.3 KiB
Text
process UCSC_BIGWIGAVERAGEOVERBED {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
|
|
conda (params.enable_conda ? "bioconda::ucsc-bigwigaverageoverbed=377" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/ucsc-bigwigaverageoverbed:377--h0b8a92a_2' :
|
|
'quay.io/biocontainers/ucsc-bigwigaverageoverbed:377--h0b8a92a_2' }"
|
|
|
|
input:
|
|
tuple val(meta), path(bed)
|
|
path bigwig
|
|
|
|
output:
|
|
tuple val(meta), path("*.tab"), emit: tab
|
|
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 VERSION = '377' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
|
// BUG: bigWigAverageOverBed cannot handle ensembl seqlevels style
|
|
"""
|
|
bigWigAverageOverBed \\
|
|
$args \\
|
|
$bigwig \\
|
|
$bed \\
|
|
${prefix}.tab
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
ucsc: $VERSION
|
|
END_VERSIONS
|
|
"""
|
|
}
|