{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/snippy/run/params.json",
    "title": "Bactopia pipeline parameters",
    "description": "A module for rapid variant calling from sequence reads",
    "type": "object",
    "definitions": {
        "snippy_parameters": {
            "title": "Snippy Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fa-solid fa-toolbox",
            "properties": {
                "reference": {
                    "type": "string",
                    "description": "Reference genome in GenBank format",
                    "fa_icon": "fas fa-angle-double-down",
                    "is_required": true
                },
                "mapqual": {
                    "type": "integer",
                    "description": "Minimum read mapping quality to consider",
                    "default": 60,
                    "fa_icon": "fas fa-angle-double-down"
                },
                "basequal": {
                    "type": "integer",
                    "description": "Minimum base quality to consider",
                    "default": 13,
                    "fa_icon": "fas fa-angle-double-down"
                },
                "mincov": {
                    "type": "integer",
                    "description": "Minimum site depth to for calling alleles",
                    "default": 10,
                    "fa_icon": "fas fa-angle-double-down",
                    "hidden": true
                },
                "minfrac": {
                    "type": "integer",
                    "description": "Minimum proportion for variant evidence (0=AUTO)",
                    "default": 0,
                    "fa_icon": "fas fa-angle-double-down",
                    "hidden": true
                },
                "minqual": {
                    "type": "integer",
                    "description": "Minimum QUALITY in VCF column 6",
                    "default": 100,
                    "fa_icon": "fas fa-angle-double-down",
                    "hidden": true
                },
                "maxsoft": {
                    "type": "integer",
                    "description": "Maximum soft clipping to allow",
                    "default": 10,
                    "fa_icon": "fas fa-angle-double-up",
                    "hidden": true
                },
                "bwaopt": {
                    "type": "string",
                    "description": "Extra BWA MEM options, eg. -x pacbio",
                    "fa_icon": "fas fa-italic"
                },
                "fbopt": {
                    "type": "string",
                    "description": "Extra Freebayes options, eg. --theta 1E-6 --read-snp-limit 2",
                    "fa_icon": "fas fa-italic"
                },
                "snippy_opts": {
                    "type": "string",
                    "description": "Extra options in quotes for Snippy",
                    "fa_icon": "fas fa-italic",
                    "hidden": false
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/snippy_parameters"
        }
    ]
}
