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55 lines
1.4 KiB
Text
55 lines
1.4 KiB
Text
nextflow.preview.dsl=2
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params.genome = ''
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process BOWTIE2 {
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// depending on the genome used one might want/need to adjust the memory settings.
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// For the E. coli test data this is probably not required
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// label 'bigMem'
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// label 'multiCore'
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input:
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tuple val(name), path(reads)
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val (outdir)
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val (bowtie2_args)
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val (verbose)
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output:
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path "*bam", emit: bam
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path "*stats.txt", emit: stats
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publishDir "$outdir/bowtie2",
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mode: "copy", overwrite: true
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script:
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if (verbose){
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println ("[MODULE] BOWTIE2 ARGS: " + bowtie2_args)
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}
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cores = 4
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readString = ""
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// Options we add are
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bowtie2_options = bowtie2_args
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bowtie2_options += " --no-unal " // We don't need unaligned reads in the BAM file
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// single-end / paired-end distinction. Might also be handled via params.single_end
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if (reads instanceof List) {
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readString = "-1 " + reads[0] + " -2 " + reads[1]
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}
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else {
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readString = "-U " + reads
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}
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index = params.genome["bowtie2"]
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bowtie2_name = name + "_" + params.genome["name"]
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println ("bowtie2 -x ${index} -p ${cores} ${bowtie2_options} ${readString} 2>${bowtie2_name}_bowtie2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> ${bowtie2_name}_bowtie2.bam")
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"""
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module load bowtie2
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module load samtools
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bowtie2 -x ${index} -p ${cores} ${bowtie2_options} ${readString} 2>${bowtie2_name}_bowtie2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> ${bowtie2_name}_bowtie2.bam
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"""
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}
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