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38 lines
1.3 KiB
Text
38 lines
1.3 KiB
Text
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process TABIX_BGZIPTABIX {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${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::tabix=0.2.6" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/tabix:0.2.6--ha92aebf_0"
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} else {
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container "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
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}
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input:
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tuple val(meta), path(input)
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output:
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tuple val(meta), path("*.gz"), path("*.tbi"), emit: tbi
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path "*.version.txt", emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bgzip -c $options.args $input > ${prefix}.gz
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tabix $options.args2 ${prefix}.gz
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echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/(.*\$//' > ${software}.version.txt
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"""
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}
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