Description

Adapter and quality trimming of sequencing reads

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

reads:file

List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

contaminants:file

Reference files containing adapter and/or contaminant sequences for sequence kmer matching

Output

name:type
description
pattern

reads

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.fastq.gz:file

The trimmed/modified fastq reads

*fastq.gz

log

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.log:file

Bbduk log file

*bbduk.log

versions

versions.yml:file

File containing software versions

versions.yml

Tools

bbmap
UC-LBL license (see package)

BBMap is a short read aligner, as well as various other bioinformatic tools.