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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
50 lines
2.2 KiB
Text
50 lines
2.2 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 METAPHLAN3 {
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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::metaphlan=3.0.10" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/metaphlan:3.0.10--pyhb7b1952_0"
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} else {
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container "quay.io/biocontainers/metaphlan:3.0.10--pyhb7b1952_0"
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}
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input:
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tuple val(meta), path(input)
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path metaphlan_db
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output:
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tuple val(meta), path("*_profile.txt") , emit: profile
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tuple val(meta), path("*.biom") , emit: biom
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tuple val(meta), path('*.bowtie2out.txt'), optional:true, emit: bt2out
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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}" : "${meta.id}"
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def input_type = ("$input".endsWith(".fastq.gz")) ? "--input_type fastq" : ("$input".contains(".fasta")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam"
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def input_data = ("$input_type".contains("fastq")) && !meta.single_end ? "${input[0]},${input[1]}" : "$input"
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def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt"
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"""
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metaphlan \\
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--nproc $task.cpus \\
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$input_type \\
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$input_data \\
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$options.args \\
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$bowtie2_out \\
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--bowtie2db ${metaphlan_db} \\
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--biom ${prefix}.biom \\
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--output_file ${prefix}_profile.txt
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echo \$(metaphlan --version 2>&1) | awk '{print \$3}' > ${software}.version.txt
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"""
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}
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