nf-core_modules/tools/fastq_screen/main.nf

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