{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/kleborate/params.json",
    "title": "Kleborate Module",
    "description": "A module to screen for MLST, sub-species, and other Klebsiella related genes of interest",
    "type": "object",
    "definitions": {
        "kleborate_parameters": {
            "title": "Kleborate Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "skip_resistance": {
                    "type": "boolean",
                    "default": false,
                    "description": "Turn off resistance genes screening",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "skip_kaptive": {
                    "type": "boolean",
                    "default": false,
                    "description": "Turn off Kaptive screening of K and O loci",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "min_identity": {
                    "type": "number",
                    "description": "Minimum alignment percent identity for main results",
                    "default": 90.0,
                    "fa_icon": "fas fa-angle-double-down",
                    "hidden": true
                },
                "kleborate_min_coverage": {
                    "type": "number",
                    "description": "Minimum alignment percent coverage for main results",
                    "default": 80.0,
                    "fa_icon": "fas fa-angle-double-down",
                    "hidden": true
                },
                "min_spurious_identity": {
                    "type": "number",
                    "description": "Minimum alignment percent identity for spurious results",
                    "default": 80.0,
                    "fa_icon": "fas fa-angle-double-down",
                    "hidden": true
                },
                "min_spurious_coverage": {
                    "type": "number",
                    "description": "Minimum alignment percent coverage for spurious results",
                    "default": 40.0,
                    "fa_icon": "fas fa-angle-double-down",
                    "hidden": true
                },
                "min_kaptive_confidence": {
                    "type": "string",
                    "default": "Good",
                    "description": "Minimum Kaptive confidence to call K/O loci - confidence levels below this will be reported as unknown",
                    "fa_icon": "fas fa-boxes",
                    "hidden": true,
                    "enum": [
                        "None",
                        "Low",
                        "Good",
                        "High",
                        "Very_high",
                        "Perfect"
                    ]
                },
                "force_index": {
                    "type": "boolean",
                    "default": false,
                    "description": "Rebuild the BLAST index at the start of execution",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/kleborate_parameters"
        }
    ]
}
