pathofact2
Description¶
Pipeline for predicting virulence Factors and toxins in protein sequences
Installation¶
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install pathofact2
Components¶
This subworkflow uses the following components:
localcdsearch/annotate(module)localcdsearch/download(module)diamond/blastp(module)diamond/makedb(module)wget(module)pathofact2/downloaddata(module)pathofact2/toxins(module)pathofact2/virulence(module)pathofact2/integrator(module)pathofact2/extractfasta(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], aminoacids, cds_gff, ips_tsv ] |
- |
ch_models |
directory | The input channel containing the path to the Pathofact2 models database directory | - |
ch_vfdb |
directory | The input channel containing the path to the Virulence Factors Database (VFDB) directory | - |
ch_cdd |
directory | The input channel containing the path to Conserved Domains Database (CDD) directory | - |
ch_zenodo_id |
string | The id of the pathofact database in zenodo | - |
meta2 |
map | Groovy Map containing the VFDB databse id e.g. [ id:'VFDB_setB_pro' ] |
- |
ch_vfdb_url |
string | The url to download VFDB using wget e.g. [[id:'VFDB_setB_pro'], 'https://www.mgc.ac.cn/VFs/Down/VFDB_setB_pro.fas.gz'] |
- |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
gff |
Channel containing a gff file with Pathofact2 annotation Structure: [ val(meta), path("*.gff") ] | - | |
versions |
file | File containing software versions Structure: [ path(versions.yml) ] | versions.yml |
