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38 lines
931 B
Text
38 lines
931 B
Text
nextflow.preview.dsl=2
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process FASTQ_SCREEN {
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publishDir "$outputdir",
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mode: "link", overwrite: true
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// depending on the number of genomes and the type of genome (e.g. plants!), memory needs to be ample!
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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 outputdir
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// fastq_screen_args are best passed in to the workflow in the following manner:
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// --fastq_screen_args="--subset 200000 --force"
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val fastq_screen_args
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val verbose
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output:
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path "*png", emit: png
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path "*html", emit: html
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path "*txt", emit: report
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script:
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println(name)
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println(reads)
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println(outputdir)
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if (verbose){
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println ("[MODULE] FASTQ SCREEN ARGS: "+ fastq_screen_args)
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}
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"""
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module load fastq_screen
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fastq_screen $fastq_screen_args $reads
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"""
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}
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