{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/genotyphi/parse/params.json",
    "title": "GenoTyphi Module",
    "description": "A module to genotype Salmonella Typhi from Mykrobe outputs",
    "type": "object",
    "definitions": {
        "genotyphi_parameters": {
            "title": "GenoTyphi Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "kmer": {
                    "type": "integer",
                    "default": 21,
                    "description": "K-mer length",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "min_depth": {
                    "type": "integer",
                    "default": 1,
                    "description": "Minimum depth",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "model": {
                    "type": "string",
                    "default": "kmer_count",
                    "description": "Genotype model used.",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true,
                    "enum": [
                        "kmer_count",
                        "median_depth"
                    ]
                },
                "report_all_calls": {
                    "type": "boolean",
                    "default": false,
                    "description": "Report all calls",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "mykrobe_opts": {
                    "type": "string",
                    "description": "Extra Mykrobe options in quotes",
                    "help": "Useful if you would like to fine tune your Mykrobne analysis.",
                    "fa_icon": "fas fa-italic"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/genotyphi_parameters"
        }
    ]
}
