kegg-pathways-completeness
Description¶
This tool computes the completeness of each KEGG pathway module for given set of KEGG orthologues (KOs) based on their presence/absence.
Keywords: KEGG, modules, pathways, orthologues
Installation¶
ebi-metagenomics/keggpathwayscompleteness
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install kegg-pathways-completeness
Tools¶
kegg-pathways-completeness¶
The tool counts completeness of each KEGG pathway for protein sequences.
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] |
- |
filtered_tbl |
file | Filtered tabulated output file from processing hmmsearch output | *.tbl |
ko_list |
file | Text file containing a list of comma-separated KO terms, to be run instead of using filtered_tbl | *.txt |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] |
- |
kegg_contigs |
file | KEGG completeness results with added contig column if fasta+hmmsearch_tbl were used | *.tsv |
kegg_pathways |
file | KEGG completeness results | *.tsv |
versions |
file | File containing software versions | versions.yml |
People¶
Authors¶
Maintainers