{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/gamma/params.json",
    "title": "GAMMA Module",
    "description": "A module for identification, classification, and annotation of translated gene matches",
    "type": "object",
    "definitions": {
        "gamma_parameters": {
            "title": "GAMMA Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "gamma_db": {
                    "type": "string",
                    "description": "A gene database (FASTA) for GAMMA",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "is_required": true
                },
                "percent_identity": {
                    "type": "integer",
                    "default": 90,
                    "description": "The minimum nucleotide sequence identiy % used by the Blat search",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "all_matches": {
                    "type": "boolean",
                    "description": "Include all gene matches, even overlaps",
                    "default": false,
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "extended": {
                    "type": "boolean",
                    "description": "Writes out all protein mutations",
                    "default": false,
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "write_fasta": {
                    "type": "boolean",
                    "description": "Write FASTA of gene matches",
                    "default": false,
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "write_gff": {
                    "type": "boolean",
                    "description": "Write gene matches as GFF file",
                    "default": false,
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/gamma_parameters"
        }
    ]
}
