{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/kraken2/params.json",
    "title": "Kraken2 Module",
    "description": "A module for taxonomic classification of sequence reads",
    "type": "object",
    "definitions": {
        "kraken2_parameters": {
            "title": "Kraken2 Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "kraken2_db": {
                    "type": "string",
                    "description": "The a single tarball or path to a Kraken2 formatted database",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "is_required": true
                },
                "quick_mode": {
                    "type": "boolean",
                    "default": false,
                    "description": "Quick operation (use first hit or hits)",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "confidence": {
                    "type": "number",
                    "default": 0.0,
                    "description": "Confidence score threshold between 0 and 1",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "minimum_base_quality": {
                    "type": "integer",
                    "default": 0,
                    "description": "Minimum base quality used in classification",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "use_mpa_style": {
                    "type": "boolean",
                    "default": false,
                    "description": "Format report output like Kraken 1's kraken-mpa-report",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "report_zero_counts": {
                    "type": "boolean",
                    "default": false,
                    "description": "Report counts for ALL taxa, even if counts are zero",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "report_minimizer_data": {
                    "type": "boolean",
                    "default": false,
                    "description": "Include minimizer and distinct minimizer count information in report",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "use_names": {
                    "type": "boolean",
                    "default": false,
                    "description": "Print scientific names instead of just taxids",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "memory_mapping": {
                    "type": "boolean",
                    "default": false,
                    "description": "Avoid loading database into RAM",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "minimum_hit_groups": {
                    "type": "integer",
                    "default": 2,
                    "description": "Minimum number of hit groups needed to make a call",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/kraken2_parameters"
        }
    ]
}
