nf-core_modules/modules/ucsc/bigwigaverageoverbed/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process UCSC_BIGWIGAVERAGEOVERBED {
tag "$meta.id"
label 'process_medium'
publishDir "${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::ucsc-bigwigaverageoverbed=377" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/ucsc-bigwigaverageoverbed:377--h0b8a92a_2"
} else {
container "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 "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
# there is a bug that bigWigAverageOverBed can not handle ensembl seqlevels style.
bigWigAverageOverBed ${options.args} $bigwig $bed ${bed.getSimpleName()}.tab
echo \$(bigWigAverageOverBed 2>&1) | sed 's/bigWigAverageOverBed v//; s/ - Compute.*\$//' > ${software}.version.txt
"""
}