{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/fastani/params.json",
    "title": "fastANI Module",
    "description": "A module for alignment-free computation Average Nucleotide Identity (ANI)",
    "type": "object",
    "definitions": {
        "fastani_parameters": {
            "title": "fastANI Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "kmer": {
                    "type": "integer",
                    "default": 16,
                    "description": "kmer size (<= 16) for ANI calculation ",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "min_fraction": {
                    "type": "number",
                    "default": 0.2,
                    "description": "Minimum fraction of genome that must be shared for trusting ANI.",
                    "help": "If reference and query genome size differ, smaller one among the two is considered.",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "frag_len": {
                    "type": "integer",
                    "default": 3000,
                    "description": "fragment length",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "skip_pairwise": {
                    "type": "boolean",
                    "default": false,
                    "description": "Only use RefSeq or local assemblies for ANI calculations",
                    "fa_icon": "fas fa-expand-arrows-alt"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/fastani_parameters"
        }
    ]
}
