cutadapt

Perform adapter/quality trimming on sequencing reads. Adapted from the nf-core cutadapt module.

nf-core modules \
  --git-remote https://github.com/CCBR/nf-modules \
  install cutadapt

https://github.com/CCBR/nf-modules/…/modules/CCBR/cutadapt/

Input

name	type	description
meta	map	Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
reads	file	List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

Output

name	type	description	pattern
meta	map	Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]	NA
reads	file	The trimmed/modified fastq reads	*fastq.gz
log	file	cuatadapt log file	*cutadapt.log
versions	file	File containing software versions	versions.yml

Tools

cuatadapt

  Docs     MIT

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.