{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/gubbins/params.json",
    "title": "Gubbins Module",
    "description": "A module for identifying recombination events in bacteria",
    "type": "object",
    "definitions": {
        "gubbins_parameters": {
            "title": "Gubbins Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "iterations": {
                    "type": "integer",
                    "description": "Maximum number of iterations",
                    "default": 5,
                    "fa_icon": "fas fa-hashtag"
                },
                "min_snps": {
                    "type": "integer",
                    "description": "Min SNPs to identify a recombination block",
                    "default": 3,
                    "fa_icon": "fas fa-hashtag",
                    "hidden": true
                },
                "min_window_size": {
                    "type": "integer",
                    "description": "Minimum window size",
                    "default": 100,
                    "fa_icon": "fas fa-hashtag",
                    "hidden": true
                },
                "max_window_size": {
                    "type": "integer",
                    "description": "Maximum window size",
                    "default": 10000,
                    "fa_icon": "fas fa-hashtag",
                    "hidden": true
                },
                "filter_percentage": {
                    "type": "number",
                    "description": "Filter out taxa with more than this percentage of gaps",
                    "default": 25.0,
                    "fa_icon": "fas fa-hashtag",
                    "hidden": true
                },
                "remove_identical_sequences": {
                    "type": "boolean",
                    "description": "Remove identical sequences",
                    "default": false,
                    "fa_icon": "fas fa-hashtag",
                    "hidden": true
                },
                "gubbin_opts": {
                    "type": "string",
                    "description": "Extra Gubbins options in quotes",
                    "help": "Useful if you would like to fine tune your Gubbins analysis. Example: '--bootstrap 100'",
                    "fa_icon": "fas fa-italic"
                },
                "skip_recombination": {
                    "type": "boolean",
                    "default": false,
                    "description": "Skip Gubbins execution in subworkflows",
                    "fa_icon": "fas fa-expand-arrows-alt"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/gubbins_parameters"
        }
    ]
}
