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60 lines
1.7 KiB
Text
60 lines
1.7 KiB
Text
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nextflow.preview.dsl=2
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params.genome = ''
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process HISAT2 {
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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 (hisat2_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/hisat2",
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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] HISAT2 ARGS: " + hisat2_args)
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}
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cores = 4
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readString = ""
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hisat_options = hisat2_args
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// Options we add are
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hisat_options = hisat_options + " --no-unal --no-softclip "
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if (reads instanceof List) {
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readString = "-1 "+reads[0]+" -2 "+reads[1]
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hisat_options = hisat_options + " --no-mixed --no-discordant"
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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["hisat2"]
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splices = ''
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if (params.genome.containsKey("hisat2_splices")){
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splices = " --known-splicesite-infile " + params.genome["hisat2_splices"]
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}
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else{
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println ("No key 'hisat2_splices' was supplied. Skipping...")
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}
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hisat_name = name + "_" + params.genome["name"]
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"""
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module load hisat2
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module load samtools
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hisat2 -p ${cores} ${hisat_options} -x ${index} ${splices} ${readString} 2>${hisat_name}_hisat2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> ${hisat_name}_hisat2.bam
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"""
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}
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