{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/emmtyper/params.json",
    "title": "emmtyper Module",
    "description": "A module for emm-typing of Streptococcus pyogenes",
    "type": "object",
    "definitions": {
        "emmtyper_parameters": {
            "title": "emmtyper Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "emmtyper_wf": {
                    "type": "string",
                    "default": "blast",
                    "description": "Workflow for emmtyper to use.",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "enum": ["blast", "pcr"]
                },
                "cluster_distance": {
                    "type": "integer",
                    "default": 500,
                    "description": "Distance between cluster of matches to consider as different clusters",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "percid": {
                    "type": "integer",
                    "default": 95,
                    "description": "Minimal percent identity of sequence",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "culling_limit": {
                    "type": "integer",
                    "default": 5,
                    "description": "Total hits to return in a position",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "mismatch": {
                    "type": "integer",
                    "default": 5,
                    "description": "Threshold for number of mismatch to allow in BLAST hit",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "align_diff": {
                    "type": "integer",
                    "default": 5,
                    "description": "Threshold for difference between alignment length and subject length in BLAST",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "gap": {
                    "type": "integer",
                    "default": 2,
                    "description": "Threshold gap to allow in BLAST hit",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "min_perfect": {
                    "type": "integer",
                    "default": 15,
                    "description": "Minimum size of perfect match at 3 primer end",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "min_good": {
                    "type": "integer",
                    "default": 15,
                    "description": "Minimum size where there must be 2 matches for each mismatch",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "max_size": {
                    "type": "integer",
                    "default": 2000,
                    "description": "Maximum size of PCR product",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/emmtyper_parameters"
        }
    ]
}
