{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/bakta/params.json",
    "title": "Bakta Module",
    "description": "A module for rapidly annotating baterial genomes",
    "type": "object",
    "definitions": {
        "bakta_parameters": {
            "title": "Bakta 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"
                },
                "replicons": {
                    "type": "string",
                    "description": "Replicon information table (tsv/csv)",
                    "fa_icon": "fas fa-file-alt"
                },
                "min_contig_length": {
                    "type": "integer",
                    "description": "Minimum contig size to annotate",
                    "default": 1,
                    "fa_icon": "fas fa-hashtag",
                    "hidden": true
                },
                "keep_contig_headers": {
                    "type": "boolean",
                    "description": "Keep original contig headers",
                    "default": false,
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "compliant": {
                    "type": "boolean",
                    "description": "Force Genbank/ENA/DDJB compliance",
                    "default": false,
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "skip_trna": {
                    "type": "boolean",
                    "description": "Skip tRNA detection & annotation",
                    "default": false,
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "skip_tmrna": {
                    "type": "boolean",
                    "description": "Skip tmRNA detection & annotation",
                    "default": false,
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "skip_rrna": {
                    "type": "boolean",
                    "description": "Skip rRNA detection & annotation",
                    "default": false,
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "skip_ncrna": {
                    "type": "boolean",
                    "description": "Skip ncRNA detection & annotation",
                    "default": false,
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "skip_ncrna_region": {
                    "type": "boolean",
                    "description": "Skip ncRNA region detection & annotation",
                    "default": false,
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "skip_crispr": {
                    "type": "boolean",
                    "description": "Skip CRISPR array detection & annotation",
                    "default": false,
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "skip_cds": {
                    "type": "boolean",
                    "description": "Skip CDS detection & annotation",
                    "default": false,
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "skip_sorf": {
                    "type": "boolean",
                    "description": "Skip sORF detection & annotation",
                    "default": false,
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "skip_gap": {
                    "type": "boolean",
                    "description": "Skip gap detection & annotation",
                    "default": false,
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "skip_ori": {
                    "type": "boolean",
                    "description": "Skip oriC/oriT detection & annotation",
                    "default": false,
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "bakta_opts": {
                    "type": "string",
                    "description": "Extra Backa options in quotes. Example: '--gram +'",
                    "help": "Useful if you would like to fine tune your Bakta analysis.",
                    "default": "",
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/bakta_parameters"
        }
    ]
}
