{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/clonalframeml/params.json",
    "title": "ClonalFrameML Module",
    "description": "A module for identifying recombination events in bacteria",
    "type": "object",
    "definitions": {
        "clonalframeml_parameters": {
            "title": "ClonalFrameML Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "emsim": {
                    "type": "integer",
                    "description": "Number of simulations to estimate uncertainty in the EM results",
                    "default": 100,
                    "fa_icon": "fas fa-hashtag"
                },
                "clonal_opts": {
                    "type": "string",
                    "description": "Extra ClonalFrameML options in quotes",
                    "help": "Useful if you would like to fine tune your ClonalFrameML analysis. Example: '-imputation_only'",
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "skip_recombination": {
                    "type": "boolean",
                    "default": false,
                    "description": "Skip ClonalFrameML execution in subworkflows",
                    "fa_icon": "fas fa-expand-arrows-alt"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/clonalframeml_parameters"
        }
    ]
}
