mgnifypipelinestoolkit_summarisegoslims
Description¶
Script that generates counts from an InterProScan output and a GO Annotation File (GAF) for both GO terms and GO-Slim terms.
Pipelines¶
This module is used by the following pipelines:
Installation¶
ebi-metagenomics/mgnifypipelinestoolkit/summarisegoslims
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install mgnifypipelinestoolkit/summarisegoslims
Tools¶
mgnifypipelinestoolkit¶
Script that summarises GO terms into GO-Slim terms, uses mgnify-pipelines-toolkit as conda environment
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] |
- |
interproscan_tsv |
file | InterProScan output tsv file. | *.tsv |
meta2 |
map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] |
- |
gaf |
file | GAF file containing the GO-slim definitions, made by Owltools. | *.gaf |
go_obo |
file | Gene ontology .OBO file, for example go-basic. Can usually be downloaded here https://geneontology.org/docs/download-ontology/ | *.go |
go_banding |
file | txt file containing the GO terms and descriptions that make up the input GO-slim | *.txt |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
go_summary |
file | - | |
goslim_summary |
file | - | |
versions |
file | - |
