bgc_annotation
Description¶
Integrates antismash, sanntis and gecco results
Installation¶
ebi-metagenomics/bgc_annotation
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install bgc_annotation
Components¶
This subworkflow uses the following components:
antismash/antismash(module)antismash/antismashdownloaddatabases(module)gecco/run(module)gecco/convert(module)antismash/json2gff(module)mgnifypipelinestoolkit/gff2gbk(module)mgnifypipelinestoolkit/bgcsmapper(module)sanntis(module)interproscan(module)
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'sample1' ] |
- |
ch_inputs |
file | The input channel containing the protein fasta file, the gff file and the interproscan tsv file e.g. [ [meta], contigs, gff, proteins, ips_annot ] |
- |
ch_antismash_db |
directory | Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory "data/databases") | - |
ch_ips_db |
directory | Directory containing interproscan database | - |
skip_sanntis |
boolean | skip sanntis (true) or run it (false) | true or false |
skip_gecco |
boolean | skip gecco (true) or run it (false) | true or false |
skip_antismash |
boolean | skip antismash (true) or run it (false) | true or false |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
gff |
Channel containing a gff file with BGCs annotation Structure: [ val(meta), path("*.gff") ] | - | |
versions |
file | File containing software versions Structure: [ path(versions.yml) ] | versions.yml |
