{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/prokka/params.json",
    "title": "Prokka Module",
    "description": "A module for annotating small genomes (bacterial, archeal, viral)",
    "type": "object",
    "definitions": {
        "prokka_parameters": {
            "title": "Prokka Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "proteins": {
                    "type": "string",
                    "description": "FASTA file of trusted proteins to first annotate from",
                    "fa_icon": "fas fa-file-alt"
                },
                "prodigal_tf": {
                    "type": "string",
                    "description": "Training file to use for Prodigal",
                    "fa_icon": "fas fa-file-alt"
                },
                "compliant": {
                    "type": "boolean",
                    "description": "Force Genbank/ENA/DDJB compliance",
                    "default": false,
                    "fa_icon": "fas fa-check",
                    "hidden": true
                },
                "centre": {
                    "type": "string",
                    "default": "Bactopia",
                    "description": "Sequencing centre ID",
                    "fa_icon": "fas fa-school",
                    "hidden": true
                },
                "prokka_coverage": {
                    "type": "integer",
                    "description": "Minimum coverage on query protein",
                    "default": 80,
                    "fa_icon": "fas fa-hashtag"
                },
                "prokka_evalue": {
                    "type": "string",
                    "description": "Similarity e-value cut-off",
                    "default": "1e-09",
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "prokka_opts": {
                    "type": "string",
                    "description": "Extra Prokka options in quotes.",
                    "default": "",
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/prokka_parameters"
        }
    ]
}
