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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
46 lines
1.4 KiB
Text
46 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 SEQTK_SUBSEQ {
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tag '$sequences'
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label 'process_low'
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publishDir "${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:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3"
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} else {
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container "quay.io/biocontainers/seqtk:1.3--h5bf99c6_3"
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}
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input:
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path sequences
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path filter_list
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output:
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path "*.gz" , emit: sequences
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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 ?: ''
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def ext = "fa"
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if ("$sequences" ==~ /.+\.fq|.+\.fq.gz|.+\.fastq|.+\.fastq.gz/) {
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ext = "fq"
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}
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"""
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seqtk \\
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subseq \\
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$options.args \\
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$sequences \\
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$filter_list | \\
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gzip --no-name > ${sequences}${prefix}.${ext}.gz
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echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//' > ${software}.version.txt
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"""
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}
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