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4ed5e4eff3
* add liftOver module * add liftover module tests * fix getProcessName * fix tests * fix out of date function * version numbers should be numeric * drop versions.yml from test.yml * Update modules/ucsc/liftover/main.nf Remove software name variable Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update tests/modules/ucsc/liftover/main.nf Use test chain file Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * add genome_chain_gz to test data config * update md5sum for new chain test data * Fix indentation in file declaration Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
48 lines
1.5 KiB
Text
48 lines
1.5 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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def VERSION = '377'
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process UCSC_LIFTOVER {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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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-liftover=377" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/ucsc-liftover:377--h0b8a92a_3"
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} else {
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container "quay.io/biocontainers/ucsc-liftover:377--h0b8a92a_3"
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}
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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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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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liftOver \\
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$options.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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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo "$VERSION")
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END_VERSIONS
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"""
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}
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