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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
44 lines
1.5 KiB
Text
44 lines
1.5 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 RAPIDNJ {
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::rapidnj=2.3.2 conda-forge::biopython=1.78" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0"
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} else {
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container "quay.io/biocontainers/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0"
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}
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input:
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path alignment
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output:
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path "*.sth" , emit: stockholm_alignment
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path "*.tre" , emit: phylogeny
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path "*.version.txt", emit: version
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script:
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def software = getSoftwareName(task.process)
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"""
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python \\
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-c 'from Bio import SeqIO; SeqIO.convert("$alignment", "fasta", "alignment.sth", "stockholm")'
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rapidnj \\
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alignment.sth \\
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$options.args \\
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-i sth \\
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-c $task.cpus \\
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-x rapidnj_phylogeny.tre
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# Doesn't appear to be a way of getting the version number
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echo 2.3.2 > ${software}.version.txt
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"""
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}
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