{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/mash/dist/params.json",
    "title": "Mash Dist Module",
    "description": "A module for calculating Mash distances between seqeunces",
    "type": "object",
    "definitions": {
        "mash_dist_parameters": {
            "title": "mashdist Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "mash_sketch": {
                    "type": "string",
                    "description": "The reference sequence as a Mash Sketch (.msh file)",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "is_required": true
                },
                "mash_seed": {
                    "type": "integer",
                    "default": 42,
                    "description": "Seed to provide to the hash function",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "mash_table": {
                    "type": "boolean",
                    "default": false,
                    "description": " Table output (fields will be blank if they do not meet the p-value threshold)",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "mash_m": {
                    "type": "integer",
                    "default": 1,
                    "description": "Minimum copies of each k-mer required to pass noise filter for reads",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "mash_w": {
                    "type": "number",
                    "default": 0.01,
                    "description": "Probability threshold for warning about low k-mer size.",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "max_p": {
                    "type": "number",
                    "default": 1.0,
                    "description": "Maximum p-value to report.",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "max_dist": {
                    "type": "number",
                    "default": 1.0,
                    "description": "Maximum distance to report.",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "merlin_dist": {
                    "type": "number",
                    "default": 0.1,
                    "description": "Maximum distance to report when using Merlin .",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "full_merlin": {
                    "type": "boolean",
                    "default": false,
                    "description": "Go full Merlin and run all species-specific tools, no matter the Mash distance",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "use_fastqs": {
                    "type": "boolean",
                    "default": false,
                    "description": "Query with FASTQs instead of the assemblies",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/mash_dist_parameters"
        }
    ]
}
