Nextflow Registry | nf-core/trimgalore@0.0.0-e3e0c68

nf-core/trimgalore @ 0.0.0-e3e0c68

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

trimming adapters sequencing fastq

Latest version: 0.0.0-e3e0c68

Total downloads: 3

Source: nf-core/modules

Authors: @drpatelh @ewels @FelixKrueger

Maintainers: @drpatelh @ewels @FelixKrueger @vagkaratzas

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

Add the following snippet to your workflow script to include this module.

include { TRIMGALORE } from 'nf-core/trimgalore'

MIT License

Process

`Name`	`TRIMGALORE`

Input 1 channel

#1 tuple

`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 6 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*report.txt` file	trimgalore log file `*report.txt`

#2 zip tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.zip` file	FastQC report output zip after trimming when the --fastqc flag is used `*_fastqc.zip`

#3 html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.html` file	FastQC HTML report after trimming when the --fastqc flag is used `*_fastqc.html`

#4 reads tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz` file	The trimmed/modified fastq reads `*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz`

#5 unpaired tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*unpaired{,_1,_2}.fq.gz` file	unpaired reads when --retain_unpaired flag is used `unpaired.fq.gz`

#6 versions_trimgalore tuple

`${task.process}` string	The name of the process
`trimgalore` string	The name of the tool
`trim_galore --version \| grep -Eo "[0-9]+(\.[0-9]+)+"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
trimgalore	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.	https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

Version	0.0.0-e3e0c68
Commit ID	e3e0c687eb5c129c011fca992af762ff2d4cb0f3
Release Date	27 Apr 2026 21:15:47 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Ftrimgalore/0.0.0-e3e0c68/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/trimgalore/blobs/sha256:4ec074f604ea0cd284a66d45f47cf5f5a8a810e6386a960a123a6d11c8a6dcde
Size	5.2 KB
Checksum	sha256:4ec074f604ea0cd284a66d45f47cf5f5a8a810e6386a960a123a6d11c8a6dcde
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-e3e0c68	27 Apr 2026 21:15:47 (UTC)		1