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458f4396a6
* Added support for `task.ext.args` * Renamed the module since it can now process any sort of BED file
38 lines
1.2 KiB
Text
38 lines
1.2 KiB
Text
process UCSC_BEDTOBIGBED {
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tag "$meta.id"
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label 'process_medium'
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
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conda (params.enable_conda ? "bioconda::ucsc-bedtobigbed=377" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/ucsc-bedtobigbed:377--h446ed27_1' :
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'quay.io/biocontainers/ucsc-bedtobigbed:377--h446ed27_1' }"
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input:
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tuple val(meta), path(bed)
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path sizes
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output:
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tuple val(meta), path("*.bigBed"), emit: bigbed
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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 ?: "${meta.id}"
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def VERSION = '377' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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bedToBigBed \\
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$bed \\
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$sizes \\
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$args \\
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${prefix}.bigBed
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cat <<-END_VERSIONS > versions.yml
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"${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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