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0745213729
* New last/mafconvert module to convert MAF alignments. The `maf-convert` tool distributed with [LAST](https://gitlab.com/mcfrith/last) reads alignmnts in [MAF](https://genome-asia.ucsc.edu/FAQ/FAQformat.html#format5) format and converts them in another format (axt, blast, blasttab, chain, gff, html, psl, sam, tab). This new module is part of the work described in Issue #464. During this development, we fix the versiob of LAST to 1219 to ensure consistency. We will upgrade it later. * Delete white space. * Update the function.nf file to the dev version.
39 lines
1.5 KiB
Text
39 lines
1.5 KiB
Text
// 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 LAST_MAFCONVERT {
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tag "$meta.id"
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label 'process_high'
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publishDir "${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::last=1219" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/last:1219--h2e03b76_0"
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} else {
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container "quay.io/biocontainers/last:1219--h2e03b76_0"
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}
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input:
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tuple val(meta), path(maf)
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output:
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tuple val(meta), path("*.{axt,blast,blasttab,chain,gff,html,psl,sam,tab}.gz"), emit: alm
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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 format = params.options.format ? params.options.format : "tab"
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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zcat $maf | maf-convert $options.args $format | gzip --no-name \\
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> ${prefix}.${format}.gz
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# maf-convert has no --version option but lastdb (part of the same package) has.
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echo \$(lastdb --version 2>&1) | sed 's/lastdb //' > ${software}.version.txt
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"""
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}
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