Description

Trim FastQ files using Trim Galore!

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

meta (map)

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

]

reads (file)

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

*{3prime,5prime,trimmed,val}*.fq.gz

unpaired (file)

FastQ files containing unpaired reads from read 1 or read 2

*unpaired*.fq.gz

html (file)

FastQC report (optional)

*_{fastqc.html}

zip (file)

FastQC report archive (optional)

*_{fastqc.zip}

log (file)

Trim Galore! trimming report

*_{report.txt}

versions (file)

File containing software versions

versions.yml
included in
atacseq chipseq circdna circrna hgtseq metatdenovo methylseq rnaseq rnasplice ssds
authors
Github user drpatelh Github user ewels Github user FelixKrueger
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

trimgalore
GPL-3.0-or-later

A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.

bioinformatics.babraham.ac.uk/projects/trim_galore github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md