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64 lines
2.3 KiB
Text
64 lines
2.3 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process BBMAP_ALIGN {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${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:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.13 pigz=2.6" : 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-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0"
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} else {
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container "quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0"
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}
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input:
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tuple val(meta), path(fastq)
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path ref
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output:
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tuple val(meta), path("*.bam"), emit: bam
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path "versions.yml" , 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}" : "${meta.id}"
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input = meta.single_end ? "in=${fastq}" : "in=${fastq[0]} in2=${fastq[1]}"
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// Set the db variable to reflect the three possible types of reference input: 1) directory
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// named 'ref', 2) directory named something else (containg a 'ref' subdir) or 3) a sequence
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// file in fasta format
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if ( ref.isDirectory() ) {
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if ( ref ==~ /(.\/)?ref\/?/ ) {
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db = ''
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} else {
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db = "path=${ref}"
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}
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} else {
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db = "ref=${ref}"
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}
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"""
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bbmap.sh \\
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$db \\
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$input \\
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out=${prefix}.bam \\
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$options.args \\
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threads=$task.cpus \\
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-Xmx${task.memory.toGiga()}g
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bbversion.sh)
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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END_VERSIONS
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"""
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}
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