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72 lines
2.9 KiB
Text
72 lines
2.9 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 BOWTIE2_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::bowtie2=2.4.2 bioconda::samtools=1.11 conda-forge::pigz=2.3.4' : 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-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0"
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} else {
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container "quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0"
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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('*.log'), 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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if (meta.single_end) {
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def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
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"""
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INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
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bowtie2 \\
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-x \$INDEX \\
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-U $reads \\
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--threads $task.cpus \\
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$unaligned \\
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$options.args \\
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2> ${prefix}.bowtie2.log \\
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| samtools view -@ $task.cpus $options.args2 -bhS -o ${prefix}.bam -
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echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt
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"""
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} else {
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def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
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"""
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INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
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bowtie2 \\
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-x \$INDEX \\
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-1 ${reads[0]} \\
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-2 ${reads[1]} \\
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--threads $task.cpus \\
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$unaligned \\
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$options.args \\
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2> ${prefix}.bowtie2.log \\
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| samtools view -@ $task.cpus $options.args2 -bhS -o ${prefix}.bam -
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if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
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mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
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fi
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if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
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mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
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fi
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echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt
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"""
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}
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}
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