nf-core_modules/modules/ucsc/bigwigaverageoverbed/main.nf
Harshil Patel 7b3315591a
Remove def software lines and emit versions channel as plural (#780)
* Remove def software line

* Replace version with versions in emit statement

* Fix default software names
2021-10-01 14:04:56 +01:00

46 lines
1.5 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
def VERSION = '377'
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 "versions.yml" , emit: versions
script:
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 \\
${prefix}.tab
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo $VERSION)
END_VERSIONS
"""
}