{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/hicap/params.json",
    "title": "hicap Module",
    "description": "A module for in-silico typing of the H. influenzae capsule locus",
    "type": "object",
    "definitions": {
        "hicap_parameters": {
            "title": "hicap Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "database_dir": {
                    "type": "string",
                    "description": "Directory containing locus database",
                    "fa_icon": "fas fa-boxes",
                    "hidden": true
                },
                "model_fp": {
                    "type": "string",
                    "description": "Path to prodigal model",
                    "fa_icon": "fas fa-boxes",
                    "hidden": true
                },
                "full_sequence": {
                    "type": "boolean",
                    "default": false,
                    "description": "Write the full input sequence out to the genbank file rather than just the region surrounding and including the locus",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "hicap_debug": {
                    "type": "boolean",
                    "default": false,
                    "description": "hicap will print debug messages",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "gene_coverage": {
                    "type": "number",
                    "description": "Minimum percentage coverage to consider a single gene complete",
                    "default": 0.8,
                    "fa_icon": "fas fa-angle-double-down"
                },
                "gene_identity": {
                    "type": "number",
                    "description": "Minimum percentage identity to consider a single gene complete",
                    "default": 0.7,
                    "fa_icon": "fas fa-angle-double-down"
                },
                "broken_gene_length": {
                    "type": "integer",
                    "description": "Minimum length to consider a broken gene",
                    "default": 60,
                    "fa_icon": "fas fa-angle-double-down"
                },
                "broken_gene_identity": {
                    "type": "number",
                    "description": "Minimum percentage identity to consider a broken gene",
                    "default": 0.8,
                    "fa_icon": "fas fa-angle-double-down"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/hicap_parameters"
        }
    ]
}
