Description

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

Input

name:type
description
pattern

meta{:bash}

:map

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

reads{:bash}

: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{:bash}

meta{:bash}

:map

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

*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz{:bash}

:file

The trimmed/modified fastq reads

*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz

log{:bash}

meta{:bash}

:map

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

*report.txt{:bash}

:file

trimgalore log file

*report.txt

unpaired{:bash}

meta{:bash}

:map

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

*unpaired{,_1,_2}.fq.gz{:bash}

:file

unpaired reads when —retain_unpaired flag is used

*unpaired*.fq.gz

html{:bash}

meta{:bash}

:map

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

*.html{:bash}

:file

FastQC HTML report after trimming when the —fastqc flag is used

*_fastqc.html

zip{:bash}

meta{:bash}

:map

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

*.zip{:bash}

:file

FastQC report output zip after trimming when the —fastqc flag is used

*_fastqc.zip

versions_trimgalore{:bash}

${task.process}{:bash}

:string

The name of the process

trimgalore{:bash}

:string

The name of the tool

trim_galore --version | grep -Eo "[0-9]+(\.[0-9]+)+"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

trimgalore{:bash}

:string

The name of the tool

trim_galore --version | grep -Eo "[0-9]+(\.[0-9]+)+"{:bash}

:eval

The expression to obtain the version of the tool

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
included in
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maintainers
Github user drpatelh
Github user ewels
Github user FelixKrueger
Github user vagkaratzas
get in touch
Ask a question on Slack Open an issue on GitHub