mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
38 lines
931 B
Text
38 lines
931 B
Text
nextflow.preview.dsl=2
|
|
|
|
process FASTQ_SCREEN {
|
|
|
|
publishDir "$outputdir",
|
|
mode: "link", overwrite: true
|
|
|
|
// depending on the number of genomes and the type of genome (e.g. plants!), memory needs to be ample!
|
|
// label 'bigMem'
|
|
// label 'multiCore'
|
|
|
|
input:
|
|
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
|
|
|
|
output:
|
|
path "*png", emit: png
|
|
path "*html", emit: html
|
|
path "*txt", emit: report
|
|
|
|
script:
|
|
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
|
|
"""
|
|
|
|
}
|