Genotype Salmonella Typhi from Mykrobe results
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
json
:file
JSON formatted file of Mykrobe results
*.json
tsv
*.tsv
A tab-delimited file of predicted genotypes
versions_genotyphi
${task.process}
:string
The name of the process
genotyphi
The name of the tool
genotyphi --version |& sed 's/^.*GenoTyphi v//'
:eval
The expression to obtain the version of the tool
versions
Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
