goslim_swf
Description¶
Get GO term and GO-slim term counts out of an InterProScan .tsv output file
Installation¶
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install goslim_swf
Pipelines¶
This subworkflow is used by the following pipelines:
Components¶
This subworkflow uses the following components:
generategaf(module)owltools(module)mgnifypipelinestoolkit/summarisegoslims(module)
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
ch_ips |
file | The input channel containing the InterProScan output file Structure: [ val(meta), path(tsv) ] | *.tsv |
go_obo |
file | Gene ontology .OBO file, for example go-basic. Can usually be downloaded here https://geneontology.org/docs/download-ontology/ | *.go |
goslim_ids |
file | txt file containing the GO terms that make up the input GO-slim | *.txt |
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 | Channel containing GO term counts Structure: [ val(meta), path(csv) ] | *_summary.csv |
goslim_summary |
file | Channel containing GO-slim term counts Structure: [ val(meta), path(csv) ] | *_slim.csv |
versions |
file | File containing software versions Structure: [ path(versions.yml) ] | versions.yml |
