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

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

This script extracts sequences in fasta format according to features described in a gff file.

genomics gff extract fasta sequence feature

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @GallVp

Maintainers: @GallVp

This script extracts sequences in fasta format according to features described in a gff file.

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

include { AGAT_SPEXTRACTSEQUENCES } from 'nf-core/agat/spextractsequences'

MIT License

Process

`Name`	`AGAT_SPEXTRACTSEQUENCES`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`gxf` file	Input GFF3/GTF file `*.{gff,gff3,gtf}`

`fasta` file	Input FASTA file `*.{fa,fsa,faa,fasta}`

`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 orignal 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 fasta tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]
`*.fasta` file	Output FASTA file. `*.fasta`

#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 18:21:17 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fagat%2Fspextractsequences/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/agat/spextractsequences/blobs/sha256:b5f067a497a5f3504b030e3a1281215db7aa345ffa4df917d8ee1a92cd85769a
Size	2.6 KB
Checksum	sha256:b5f067a497a5f3504b030e3a1281215db7aa345ffa4df917d8ee1a92cd85769a
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:21:17 (UTC)		1	2.6 KB	-