{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/busco/params.json",
    "title": "BUSCO  Module",
    "description": "A module for assessing genome assembly and annotation completeness",
    "type": "object",
    "definitions": {
        "busco_parameters": {
            "title": "BUSCO Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "busco_lineage": {
                    "type": "string",
                    "default": "bacteria_odb10",
                    "description": "Specify the name of the BUSCO lineage to be used",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "busco_evalue": {
                    "type": "string",
                    "default": "1e-03",
                    "description": "E-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e-03",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "busco_limit": {
                    "type": "integer",
                    "default": 3,
                    "description": "Total candidate regions to consider per BUSCO",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "metaeuk_parameters": {
                    "type": "string",
                    "default": "",
                    "description": "Additional Metaeuk first-pass arguments contained within a single pair of quotation marks, separated by commas",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "metaeuk_rerun_parameters": {
                    "type": "string",
                    "default": "",
                    "description": "Additional Metaeuk second-pass arguments contained within a single pair of quotation marks, separated by commas",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "use_augustus": {
                    "type": "boolean",
                    "default": false,
                    "description": "Use augustus gene predictor for eukaryote runs",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "augustus_parameters": {
                    "type": "string",
                    "default": "",
                    "description": "Additional Augustus arguments contained within a single pair of quotation marks, separated by commas",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "augustus_species": {
                    "type": "string",
                    "default": "",
                    "description": "Specify a species for Augustus training",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "augustus_long": {
                    "type": "boolean",
                    "default": false,
                    "description": "Optimization Augustus self-training mode",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/busco_parameters"
        }
    ]
}
