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41 lines
1.1 KiB
Text
41 lines
1.1 KiB
Text
def VERSION = '377' // Version information not provided by tool on CLI
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process UCSC_LIFTOVER {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::ucsc-liftover=377" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/ucsc-liftover:377--h0b8a92a_3' :
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'quay.io/biocontainers/ucsc-liftover:377--h0b8a92a_3' }"
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input:
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tuple val(meta), path(bed)
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path(chain)
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output:
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tuple val(meta), path("*.lifted.bed") , emit: lifted
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tuple val(meta), path("*.unlifted.bed"), emit: unlifted
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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 ?: "${meta.id}"
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"""
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liftOver \\
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$args \
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$bed \\
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$chain \\
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${prefix}.lifted.bed \\
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${prefix}.unlifted.bed
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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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