nf-core_modules/modules/ucsc/bigwigaverageoverbed/main.nf
2022-06-27 10:35:41 +02:00

39 lines
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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
"""
}