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71 lines
2.9 KiB
Text
71 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 STAR_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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// Note: 2.7X indices incompatible with AWS iGenomes.
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conda (params.enable_conda ? 'bioconda::star=2.6.1d' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container 'https://depot.galaxyproject.org/singularity/star:2.6.1d--0'
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} else {
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container 'quay.io/biocontainers/star:2.6.1d--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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path gtf
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output:
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tuple val(meta), path('*d.out.bam') , emit: bam
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tuple val(meta), path('*Log.final.out') , emit: log_final
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tuple val(meta), path('*Log.out') , emit: log_out
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tuple val(meta), path('*Log.progress.out'), emit: log_progress
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path '*.version.txt' , emit: version
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tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted
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tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript
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tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted
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tuple val(meta), path('*fastq.gz') , optional:true, emit: fastq
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tuple val(meta), path('*.tab') , optional:true, emit: tab
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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 ignore_gtf = params.star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
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def seq_center = params.seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$params.seq_center' 'SM:$prefix'" : "--outSAMattrRGline ID:$prefix 'SM:$prefix'"
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def out_sam_type = (options.args.contains('--outSAMtype')) ? '' : '--outSAMtype BAM Unsorted'
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def mv_unsorted_bam = (options.args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : ''
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"""
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STAR \\
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--genomeDir $index \\
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--readFilesIn $reads \\
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--runThreadN $task.cpus \\
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--outFileNamePrefix $prefix. \\
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$out_sam_type \\
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$ignore_gtf \\
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$seq_center \\
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$options.args
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$mv_unsorted_bam
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if [ -f ${prefix}.Unmapped.out.mate1 ]; then
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mv ${prefix}.Unmapped.out.mate1 ${prefix}.unmapped_1.fastq
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gzip ${prefix}.unmapped_1.fastq
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fi
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if [ -f ${prefix}.Unmapped.out.mate2 ]; then
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mv ${prefix}.Unmapped.out.mate2 ${prefix}.unmapped_2.fastq
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gzip ${prefix}.unmapped_2.fastq
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fi
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STAR --version | sed -e "s/STAR_//g" > ${software}.version.txt
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"""
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}
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