mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
34 lines
1 KiB
Text
34 lines
1 KiB
Text
/*
|
|
* Description:
|
|
* Run FastQC on sequenced reads
|
|
* Keywords:
|
|
* read qc
|
|
* adapter
|
|
* Tools:
|
|
* FastQC:
|
|
* homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
|
|
* documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
|
|
* description: FastQC gives general quality metrics about your reads.
|
|
* It provides information about the quality score distribution
|
|
* across your reads, the per base sequence content (%A/C/G/T).
|
|
* You get information about adapter contamination and other
|
|
* overrepresented sequences.
|
|
*/
|
|
process fastqc {
|
|
tag "$sample_id"
|
|
publishDir "${params.outdir}/fastqc", mode: 'copy',
|
|
saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"}
|
|
|
|
input:
|
|
set val(sample_id), file(reads)
|
|
|
|
output:
|
|
file "*_fastqc.{zip,html}"
|
|
|
|
script:
|
|
"""
|
|
fastqc -q $reads
|
|
|
|
fastqc --version &> fastqc.version.txt
|
|
"""
|
|
}
|