{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/pirate/params.json",
    "title": "PIRATE Module",
    "description": "A module for determining the building a pangenome",
    "type": "object",
    "definitions": {
        "pirate_parameters": {
            "title": "PIRATE Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "steps": {
                    "type": "string",
                    "default": "50,60,70,80,90,95,98",
                    "description": "Percent identity thresholds to use for pangenome construction",
                    "fa_icon": "fas fa-italic"
                },
                "features": {
                    "type": "string",
                    "default": "CDS",
                    "description": "Comma-delimited features to use for pangenome construction",
                    "fa_icon": "fas fa-italic"
                },
                "para_off": {
                    "type": "boolean",
                    "default": false,
                    "description": "Switch off paralog identification",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "z": {
                    "type": "boolean",
                    "default": false,
                    "description": "Retain all PIRATE intermediate files",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "pan_opt": {
                    "type": "string",
                    "description": "Additional arguments to pass to pangenome contruction.",
                    "help": "PLease see https://github.com/SionBayliss/PIRATE#advanced-examples for more details",
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/pirate_parameters"
        }
    ]
}
