Description

Genotype Salmonella Typhi from Mykrobe results

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

json (file)

JSON formatted file of Mykrobe results

*.json

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

tsv (file)

A tab-delimited file of predicted genotypes

*.tsv

Tools

genotyphi
GPL v3

Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)