nf-core/agat/convertspgxf2gxf @ 0.0.0-0c7146d
Summary
Fixes and standardizes GFF/GTF files and outputs a cleaned GFF/GTF file
Get started
Add the following snippet to your workflow script to include this module.
include { AGAT_CONVERTSPGXF2GXF } from 'nf-core/agat/convertspgxf2gxf'
License
MIT License
Process
Name
|
AGAT_CONVERTSPGXF2GXF |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
gxf
file
|
Annotation file in GFF3/GTF format *.{gff, gtf}
|
Output
2 channels
#1
output_gff
tuple
meta
map
|
Groovy Map containing sample information |
|---|---|
*.agat.gff
file
|
Cleaned annotation file in GFF3 format *.{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 | AGAT is a toolkit for manipulation and getting information from GFF/GTF files | https://github.com/NBISweden/AGAT |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:21:14 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fagat%2Fconvertspgxf2gxf/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/agat/convertspgxf2gxf/blobs/sha256:45bcf520501de60106ef1cc20488868c43282c0922778fb4d51fc7ef525536e2 |
| Size | 2.1 KB |
| Checksum | sha256:45bcf520501de60106ef1cc20488868c43282c0922778fb4d51fc7ef525536e2 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:21:14 (UTC) | 1 | 2.1 KB | - |