nf-core/agat/spflagshortintrons @ 0.0.0-0c7146d
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)
| 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/ |
Input
2 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}
|
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
gff
tuple
meta
map
|
Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ] |
|---|---|
*.gff
file
|
Output GFF file.
*.{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 |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 0c7146d85582628b5d1034504702fa808632b1af |
| Release Date | 08 Apr 2026 18:41:47 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fagat%2Fspflagshortintrons/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/agat/spflagshortintrons/blobs/sha256:f90063fd8e127040c25f51cbf6bd28160e633172a8d36dca5478b4e2d4458b28 |
| Size | 2.7 KB |
| Checksum | sha256:f90063fd8e127040c25f51cbf6bd28160e633172a8d36dca5478b4e2d4458b28 |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:41:47 (UTC) | PUBLISHED | 4 | 2.7 KB |