Description

Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates

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.

Output

name:type
description
pattern

reads

meta:map

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

]

*.fastq.gz:file

The reordered/clumped (and if necessary deduped) fastq reads

*.clumped.fastq.gz

log

meta:map

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

]

*.log:file

Clumpify log file

*clumpify.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.