Nextflow Registry | nf-core/agat/spkeeplongestisoform@0.0.0-6c4ed3a

nf-core/agat/spkeeplongestisoform @ 0.0.0-6c4ed3a

Filters GFF records to keep only the longest isoform per gene

gff gtf filter isoform gene longest agat

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @Juke34

Maintainers: @Juke34

Filters GFF records to keep only the longest isoform per gene

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

include { AGAT_SPKEEPLONGESTISOFORM } from 'nf-core/agat/spkeeplongestisoform'

MIT License

Process

`Name`	`AGAT_SPKEEPLONGESTISOFORM`

Input 2 channels

#1 tuple

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

`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`
`${output}` file	Output GFF3 file `*.longest.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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:01:49 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fagat%2Fspkeeplongestisoform/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/agat/spkeeplongestisoform/blobs/sha256:a9d7f969831ec6592c0bf4bdc9bb3d0d55a851fd0fd87d6ef9e87559c53042de
Size	2.6 KB
Checksum	sha256:a9d7f969831ec6592c0bf4bdc9bb3d0d55a851fd0fd87d6ef9e87559c53042de
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:01:49 (UTC)	3	2.6 KB
0.0.0-3fc6d40	22 Apr 2026 15:01:21 (UTC)	3	2.6 KB
0.0.0-0c7146d	08 Apr 2026 18:41:49 (UTC)	3	2.6 KB