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4575e5455c
* New last/split module to find split alignments. The `last-split` tool distributed with [LAST](https://gitlab.com/mcfrith/last) finds split or spliced alignments in a MAF file that is produced with, for example, LAST `lastal` command. This new module is part of the work discribed in Issue #464. During this development, we fix the versiob of LAST to 1219 to ensure consistency. We will upgrade it later. * Update software/last/split/main.nf * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
36 lines
1.3 KiB
Text
36 lines
1.3 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_SPLIT {
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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("*.maf.gz"), emit: maf
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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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zcat $maf | last-split $options.args | gzip --no-name > ${prefix}.maf.gz
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echo \$(last-split --version 2>&1) | sed 's/last-split //' > ${software}.version.txt
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"""
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}
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