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goslim_swf

Description

Get GO term and GO-slim term counts out of an InterProScan .tsv output file

Installation

ebi-metagenomics/goslim_swf

nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install goslim_swf

Keywords: GO, GO-slim, interpro, interproscan, owltools

Components

This subworkflow uses the following components:

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

People

Authors

Maintainers