mirror of
https://github.com/MillironX/nf-core_modules.git
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56 lines
2 KiB
Text
56 lines
2 KiB
Text
process BOWTIE_ALIGN {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.11' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0' :
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'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0' }"
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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 "versions.yml" , emit: versions
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tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
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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 args2 = task.ext.args2 ?: ''
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def prefix = task.ext.prefix ?: "${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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$args \\
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$endedness \\
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2> ${prefix}.out \\
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| samtools view $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 ${prefix}.unmapped_2.fastq
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fi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bowtie: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//')
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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