nf-core/agat/spmergeannotations @ 0.0.0-3fc6d40
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
Name
|
AGAT_SPMERGEANNOTATIONS |
|---|
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
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
|
|---|
gff
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.gff
file
|
Output GFF file. *.gff
|
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 | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:01:22 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fagat%2Fspmergeannotations/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/agat/spmergeannotations/blobs/sha256:852d90a584dad6707a80d27f99863c2bf3c5e8244ebedf87d9ee7e64f9eee590 |
| Size | 2.9 KB |
| Checksum | sha256:852d90a584dad6707a80d27f99863c2bf3c5e8244ebedf87d9ee7e64f9eee590 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:01:50 (UTC) | 4 | 2.9 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:01:22 (UTC) | 3 | 2.9 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:41:51 (UTC) | 4 | 2.8 KB |