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59 lines
2.2 KiB
Text
59 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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def options = initOptions(params.options)
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process BOWTIE_ALIGN {
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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), publish_id:meta.id) }
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conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.10' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container 'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0'
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} else {
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container 'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0'
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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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tuple val(meta), path('*.out'), emit: log
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path '*.version.txt' , emit: version
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tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
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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 unaligned = params.save_unaligned ? "--un ${prefix}.unmapped.fastq" : ''
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def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}"
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"""
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INDEX=`find -L ./ -name "*.3.ebwt" | sed 's/.3.ebwt//'`
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bowtie \\
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--threads $task.cpus \\
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--sam \\
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-x \$INDEX \\
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-q \\
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$unaligned \\
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$options.args \\
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$endedness \\
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2> ${prefix}.out \\
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| samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
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if [ -f ${prefix}.unmapped.fastq ]; then
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gzip ${prefix}.unmapped.fastq
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fi
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if [ -f ${prefix}.unmapped_1.fastq ]; then
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gzip ${prefix}.unmapped_1.fastq
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gzip ${prefix}.unmapped_2.fastq
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fi
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echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//' > ${software}.version.txt
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"""
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}
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