pathofact2_virulence
Description¶
Pathofact2 - Machine Learning tool to predict virulence factors in protein sequences
Installation¶
ebi-metagenomics/pathofact2/virulence
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install pathofact2/virulence
Tools¶
pathofact2¶
PathoFact 2.0, an enhanced pipeline for improved ARG, VF, and toxin prediction in prokaryotic protein sequences
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'sample1' ] |
- |
fasta |
file | Protein sequences in FASTA format | *{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz} |
pathofact2_db |
directory | Pathofact2 database. Can be either: - A compressed tarball (.tar.gz) that will be extracted - An uncompressed directory containing the models | *.{tar.gz,} |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
tsv |
file | - | |
versions_python |
file | - | |
versions_pathofact2 |
file | - |
