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ca321ce69d
The `last-postmask` tool distributed with [LAST](https://gitlab.com/mcfrith/last) filters alignments in a MAF file to remove those with too many masked (lower-case) positions compared with their score. As other filter modules like `last/split`, its output file risks to overwrite its input file as their names are constructed from the sample ID when multiple filters are chained in the pipeline. I added a check that gives a clearer error message in this case. Please let me know what you think about; I can add this test to the existing LAST modules as well. This new module is part of the work discribed in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency. We will upgrade it later.
38 lines
1.4 KiB
Text
38 lines
1.4 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_POSTMASK {
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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::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}" : "${meta.id}"
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if( "$maf" == "${prefix}.maf.gz" ) error "Input and output names are the same, use the suffix option to disambiguate"
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"""
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zcat $maf | last-postmask $options.args | gzip --no-name > ${prefix}.maf.gz
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# last-postmask does not have a --version option
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echo \$(lastal --version 2>&1) | sed 's/lastal //' > ${software}.version.txt
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"""
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}
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