pathofact2_extractfasta
Description¶
Extract the fasta file of the proteins predicted by Pathofact2 for annotation using rpsblast vs CDD
Installation¶
ebi-metagenomics/pathofact2/extractfasta
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install pathofact2/extractfasta
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} |
blastp_out |
file | Result of diamond blastp vs VFDB. Columns qseqid sseqid pident length qlen slen evalue bitscore | *.{txt,txt.gz} |
pathofact2_tox |
file | Result of Pathofact2 toxins prediction | *.{tsv,tsv.gz} |
pathofact2_vf |
file | Result of Pathofact2 virulence factors prediction | *.{tsv,tsv.gz} |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
fasta |
file | - | |
tsv |
file | - | |
versions_python |
file | - | |
versions_pathofact2 |
file | - |
