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e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
47 lines
1.6 KiB
Text
47 lines
1.6 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_LASTAL {
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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=1238" : 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:1238--h2e03b76_0"
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} else {
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container "quay.io/biocontainers/last:1238--h2e03b76_0"
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}
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input:
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tuple val(meta), path(fastx), path (param_file)
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path index
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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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def trained_params = param_file ? "-p ${param_file}" : ''
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"""
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INDEX_NAME=\$(basename \$(ls $index/*.des) .des)
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lastal \\
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$trained_params \\
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$options.args \\
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-P $task.cpus \\
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${index}/\$INDEX_NAME \\
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$fastx \\
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| gzip --no-name > ${prefix}.\$INDEX_NAME.maf.gz
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# gzip needs --no-name otherwise it puts a timestamp in the file,
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# which makes its checksum non-reproducible.
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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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