Nextflow Registry | nf-core/trimgalore@0.0.0-c4ed7fd

nf-core/trimgalore @ 0.0.0-c4ed7fd

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-c4ed7fd

Total downloads: 9

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-c4ed7fd
Commit ID	c4ed7fdd281d290c622c5d93fa173effc0217fdb
Release Date	27 Apr 2026 15:00:29 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Ftrimgalore/0.0.0-c4ed7fd/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/trimgalore/blobs/sha256:a76297a4082c2319a79eb91cd24f9e6ea5a84904dbe4e201fb1265c6fbf70acc
Size	5.3 KB
Checksum	sha256:a76297a4082c2319a79eb91cd24f9e6ea5a84904dbe4e201fb1265c6fbf70acc
Downloads	0

Version	Date	Status	Downloads	Size
0.0.0-c4ed7fd	27 Apr 2026 15:00:29 (UTC)		0	5.3 KB