Nextflow Registry | nf-core/agat/spmergeannotations@0.0.0-0c7146d

nf-core/agat/spmergeannotations @ 0.0.0-0c7146d

This script merge different gff annotation files in one. It uses the AGAT parser that takes care of duplicated names and fixes other oddities met in those files.

genomics gff merge combine

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @GallVp

Maintainers: @GallVp

Summary

This script merge different gff annotation files in one. It uses the AGAT parser that takes care of duplicated names and fixes other oddities met in those files.

Get started

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

include { AGAT_SPMERGEANNOTATIONS } from 'nf-core/agat/spmergeannotations'

License

MIT License

Process

`Name`	`AGAT_SPMERGEANNOTATIONS`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`gffs` list	A list of GFFs to merge `[ *.{gff,gff3} ]`

`config` file	Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). `*.yaml`

Output 2 channels

#1 gff tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.gff` file	Output GFF file. `*.gff`

#2 versions_agat tuple

`${task.process}` string	The name of the process
`agat` string	The name of the tool
`agat --version \| sed 's/v//'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
agat	Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.	https://agat.readthedocs.io/en/latest/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:21:27 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fagat%2Fspmergeannotations/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/agat/spmergeannotations/blobs/sha256:2b0feeaba35aa8337982d71dca849a6b865a6b1bd7535ebf60847be36f6fa6a4
Size	2.8 KB
Checksum	sha256:2b0feeaba35aa8337982d71dca849a6b865a6b1bd7535ebf60847be36f6fa6a4
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:21:27 (UTC)		1	2.8 KB	-