nf-core/agat/spflagshortintrons @ 0.0.0-0c7146d
Summary
The script flags the short introns with the attribute . Is is usefull to avoid ERROR when submiting the data to EBI. (Typical EBI error message: ********ERROR: Intron usually expected to be at least 10 nt long. Please check the accuracy)
Get started
Add the following snippet to your workflow script to include this module.
include { AGAT_SPFLAGSHORTINTRONS } from 'nf-core/agat/spflagshortintrons'
License
MIT License
Name
|
AGAT_SPFLAGSHORTINTRONS |
|---|
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
gxf
file
|
Input GFF3/GTF file *.{gff,gff3,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 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}
|
|---|
gff
tuple
meta
map
|
Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ] |
|---|---|
*.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 | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:21:24 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fagat%2Fspflagshortintrons/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/agat/spflagshortintrons/blobs/sha256:8b3b0254cad76747e17ebb9af121a665c369118c6459a4457cbf65f89c08d5ba |
| Size | 2.8 KB |
| Checksum | sha256:8b3b0254cad76747e17ebb9af121a665c369118c6459a4457cbf65f89c08d5ba |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:21:24 (UTC) | 1 | 2.8 KB | - |