{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/mashtree/params.json",
    "title": "Mashtree Module",
    "description": "A module to create a tree using Mash distance",
    "type": "object",
    "definitions": {
        "mashtree_parameters": {
            "title": "Mashtree Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "trunclength": {
                    "type": "integer",
                    "description": "How many characters to keep in a filename",
                    "default": 250,
                    "fa_icon": "fas fa-angle-double-down",
                    "hidden": true
                },
                "sortorder": {
                    "type": "string",
                    "default": "ABC",
                    "description": "For neighbor-joining, the sort order can make a difference.",
                    "fa_icon": "fas fa-boxes",
                    "enum": [
                        "ABC",
                        "random",
                        "input-order"
                    ]
                },
                "genomesize": {
                    "type": "integer",
                    "description": "Genome size of the input samples",
                    "default": 5000000,
                    "fa_icon": "fas fa-angle-double-down"
                },
                "mindepth": {
                    "type": "integer",
                    "description": "If mindepth is zero, then it will be chosen in a smart but slower method, to discard lower-abundance kmers.",
                    "default": 5,
                    "fa_icon": "fas fa-angle-double-down"
                },
                "kmerlength": {
                    "type": "integer",
                    "description": "Hashes will be based on strings of this many nucleotides",
                    "default": 21,
                    "fa_icon": "fas fa-angle-double-down"
                },
                "sketchsize": {
                    "type": "integer",
                    "description": "Each sketch will have at most this many non-redundant min-hashes",
                    "default": 10000,
                    "fa_icon": "fas fa-angle-double-down",
                    "hidden": true
                },
                "save_sketches": {
                    "type": "boolean",
                    "default": false,
                    "description": "Save sketches created during the process",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/mashtree_parameters"
        }
    ]
}
