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

46 lines
1.3 KiB
Text
Raw Normal View History

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
def VERSION = '377' // No version information printed
process UCSC_WIGTOBIGWIG {
tag '$wig'
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::ucsc-wigtobigwig=377" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/ucsc-wigtobigwig:377--h0b8a92a_2"
} else {
container "quay.io/biocontainers/ucsc-wigtobigwig:377--h0b8a92a_2"
}
input:
path wig
path chromsizes
output:
path "*.bw" , emit: bw
path "versions.yml" , emit: versions
script:
"""
wigToBigWig \\
$options.args \\
$wig \\
$chromsizes \\
${wig.getSimpleName()}.bw
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo "$VERSION")
END_VERSIONS
"""
}