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62 lines
2.3 KiB
Plaintext
62 lines
2.3 KiB
Plaintext
process CENTRIFUGE_CENTRIFUGE {
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tag "$meta.id"
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label 'process_high'
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conda "bioconda::centrifuge=1.0.4_beta"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' :
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'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
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input:
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tuple val(meta), path(reads)
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path db
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val save_unaligned
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val save_aligned
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val sam_format
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output:
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tuple val(meta), path('*report.txt') , emit: report
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tuple val(meta), path('*results.txt') , emit: results
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tuple val(meta), path('*.sam') , optional: true, emit: sam
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tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_mapped
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tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
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def unaligned = ''
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def aligned = ''
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if (meta.single_end) {
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unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
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aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
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} else {
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unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
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aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
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}
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def sam_output = sam_format ? "--out-fmt 'sam'" : ''
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"""
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## we add "-no-name ._" to ensure silly Mac OSX metafiles files aren't included
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db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/\\.1.cf\$//'`
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centrifuge \\
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-x \$db_name \\
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-p $task.cpus \\
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$paired \\
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--report-file ${prefix}.report.txt \\
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-S ${prefix}.results.txt \\
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$unaligned \\
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$aligned \\
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$sam_output \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //')
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END_VERSIONS
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"""
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}
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