{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/roary/params.json",
    "title": "Roary Module",
    "description": "A module for building a pangenome",
    "type": "object",
    "definitions": {
        "roary_parameters": {
            "title": "Roary Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "use_prank": {
                    "type": "boolean",
                    "default": false,
                    "description": "Use PRANK instead of MAFFT for core gene",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "use_roary": {
                    "type": "boolean",
                    "default": false,
                    "description": "Use Roary instead of PIRATE in the 'pangenome' subworkflow",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "i": {
                    "type": "integer",
                    "default": 95,
                    "description": "Minimum percentage identity for blastp",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "cd": {
                    "type": "integer",
                    "default": 99,
                    "description": "Percentage of isolates a gene must be in to be core",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "g": {
                    "type": "integer",
                    "default": 50000,
                    "description": "Maximum number of clusters",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "s": {
                    "type": "boolean",
                    "default": false,
                    "description": "Do not split paralogs",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "ap": {
                    "type": "boolean",
                    "default": false,
                    "description": "Allow paralogs in core alignment",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "iv": {
                    "type": "number",
                    "default": 1.5,
                    "description": "MCL inflation value",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/roary_parameters"
        }
    ]
}
