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6913da9d2d
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Start MALT-build * Start MALT build (missing meta files and outputs specS) * Local tests * Correct test map_type * Finished module, just waiting for UNZIP module to finalise tests * Correct tests in preparation for Unzip * Ouptut log file too * Update meta.yml * Rename log file * Rename log file * Remove debugging stuff * Add Unzip module * Linting update * Linting update * Fix input db * Fix db file in cmd * Update modules/malt/build/main.nf * Update modules/malt/build/main.nf * Update main.nf
58 lines
1.9 KiB
Text
58 lines
1.9 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 MALT_BUILD {
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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:[:], publish_by_meta:[]) }
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// Do not **auto-bump** due to problem with change of version numbering between 0.4.1 and 0.5.2
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// (originally 0.4.1 was listed as 0.41, so is always selected as 'latest' even though it is not!)
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conda (params.enable_conda ? "bioconda::malt=0.5.2" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/malt:0.5.2--0"
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} else {
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container "quay.io/biocontainers/malt:0.5.2--0"
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}
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input:
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path fastas
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val seq_type
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path gff
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path map_db
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output:
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path "malt_index/" , emit: index
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path "*.version.txt" , emit: version
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path "malt-build.log", emit: log
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script:
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def software = getSoftwareName(task.process)
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def avail_mem = 6
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if (!task.memory) {
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log.info '[MALT_BUILD] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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def igff = gff ? "-igff ${gff}" : ""
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"""
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malt-build \\
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-J-Xmx${avail_mem}g \\
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-v \\
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--input ${fastas.join(' ')} \\
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-s $seq_type \\
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$igff \\
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-d 'malt_index/' \\
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-t ${task.cpus} \\
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$options.args \\
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-mdb ${map_db}/*.db |&tee malt-build.log
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malt-build --help |& tail -n 3 | head -n 1 | cut -f 2 -d'(' | cut -f 1 -d ',' | cut -d ' ' -f 2 > ${software}.version.txt
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"""
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}
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