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39 lines
1.1 KiB
Text
39 lines
1.1 KiB
Text
def VERSION = '377' // Version information not provided by tool on CLI
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process UCSC_BIGWIGAVERAGEOVERBED {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::ucsc-bigwigaverageoverbed=377" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/ucsc-bigwigaverageoverbed:377--h0b8a92a_2' :
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'quay.io/biocontainers/ucsc-bigwigaverageoverbed:377--h0b8a92a_2' }"
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input:
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tuple val(meta), path(bed)
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path bigwig
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output:
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tuple val(meta), path("*.tab"), emit: tab
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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// BUG: bigWigAverageOverBed cannot handle ensembl seqlevels style
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"""
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bigWigAverageOverBed \\
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$args \\
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$bigwig \\
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$bed \\
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${prefix}.tab
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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ucsc: $VERSION
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END_VERSIONS
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"""
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}
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