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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
1.7 KiB
Text
47 lines
1.7 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 BWAMEM2_MEM {
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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::bwa-mem2=2.2.1 bioconda::samtools=1.12" : 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-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0"
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} else {
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container "quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0"
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}
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input:
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tuple val(meta), path(reads)
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path index
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output:
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tuple val(meta), path("*.bam"), emit: bam
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path "*.version.txt" , emit: version
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script:
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def split_cpus = Math.floor(task.cpus/2)
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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 read_group = meta.read_group ? "-R ${meta.read_group}" : ""
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"""
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INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
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bwa-mem2 mem \\
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$options.args \\
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$read_group \\
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-t ${split_cpus} \\
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\$INDEX \\
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$reads \\
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| samtools view $options.args2 -@ ${split_cpus} -bhS -o ${prefix}.bam -
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echo \$(bwa-mem2 version 2>&1) > ${software}.version.txt
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"""
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}
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