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

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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def VERSION = '377'
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process UCSC_BEDGRAPHTOBIGWIG {
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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']) }
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conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1"
} else {
container "quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1"
}
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input:
tuple val(meta), path(bedgraph)
path sizes
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output:
tuple val(meta), path("*.bigWig"), emit: bigwig
path "versions.yml" , emit: versions
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script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
bedGraphToBigWig \\
$bedgraph \\
$sizes \\
${prefix}.bigWig
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo $VERSION)
END_VERSIONS
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"""
}