pathofact2_integrator
Description¶
Module to integrate Pathofact2 results with CDD annotations into a single GFF file
Installation¶
ebi-metagenomics/pathofact2/integrator
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install pathofact2/integrator
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' ] |
- |
gff |
file | The GFF3 file corresponding to the annotated genes | *.{gff,gff.gz} |
prot_annot |
file | Tab-delimited file of functional annotation. It can be the interproscan result for all the proteins provided by the user or the CDD annotation for relevant proteins generated as part of the pathofact subworkflow | *.{tsv,tsv.gz} |
pathofact_support |
file | Tab-delimited file corresponding to the Pathofact2 result | *.{tsv} |
annot_type |
string | Annotation type to be parsed. Valid strings are 'cdd' for results generated in the subworkflow by local-cd-search module or 'ips' for user provided interproscan annotation | cdd|ips |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
gff |
file | - | |
versions_python |
file | - | |
versions_pathofact2 |
file | - |
