{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/gtdbtk/classifywf/params.json",
    "title": "GTDB Classify Module",
    "description": "Identify marker genes and assign taxonomic classifications",
    "type": "object",
    "definitions": {
        "gtdb_classifywf_parameters": {
            "title": "GTDB Classify Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "min_af": {
                    "type": "number",
                    "default": 0.65,
                    "description": "Minimum alignment fraction to consider closest genome",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "min_perc_aa": {
                    "type": "integer",
                    "default": 10,
                    "description": "Filter genomes with an insufficient percentage of AA in the MSA",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "gtdb_tmp": {
                    "type": "boolean",
                    "default": "/tmp",
                    "description": "Specify alternative directory for temporary files",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "gtdb_use_scratch": {
                    "type": "boolean",
                    "default": false,
                    "description": "Reduce pplacer memory usage by writing to --gtdb_tmp location (slower)",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "gtdb_debug": {
                    "type": "boolean",
                    "default": false,
                    "description": "Create intermediate files for debugging purposes",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "force_gtdb": {
                    "type": "boolean",
                    "default": false,
                    "description": "Continue processing if an error occurs on a single genome",
                    "fa_icon": "fas fa-expand-arrows-alt"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/gtdb_classifywf_parameters"
        }
    ]
}
