nf-core_modules/software/fastqc/main.nf
2020-07-11 14:27:21 +02:00

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Text

nextflow.preview.dsl = 2
process FASTQC {
// tag "FastQC - $sample_id"
input:
tuple val(name), path(reads)
val (outputdir)
// fastqc_args are best passed into the workflow in the following manner:
// --fastqc_args="--nogroup -a custom_adapter_file.txt"
val (fastqc_args)
val (verbose)
output:
tuple val(name), path ("*fastqc*"), emit: all
path "*.zip", emit: report // e.g. for MultiQC later
// container 'quay.io/biocontainers/fastqc:0.11.8--2'
publishDir "$outputdir",
mode: "copy", overwrite: true
script:
if (verbose){
println ("[MODULE] FASTQC ARGS: " + fastqc_args)
}
"""
module load fastqc
fastqc $fastqc_args -q -t 2 $reads
fastqc --version &> fastqc.version.txt
"""
}