{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/tbprofiler/profile/params.json",
    "title": "TBProfiler Module",
    "description": "A module to detect resistance and lineages of Mycobacterium tuberculosis genomes",
    "type": "object",
    "definitions": {
        "tbprofiler_parameters": {
            "title": "TBProfiler Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "call_whole_genome": {
                    "type": "boolean",
                    "default": false,
                    "description": "Call whole genome",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "mapper": {
                    "type": "string",
                    "default": "bwa",
                    "description": "Mapping tool to use. If you are using nanopore data it will default to minimap2",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true,
                    "enum": ["bwa", "minimap2", "bowtie2", "bwa-mem2"]
                },
                "caller": {
                    "type": "string",
                    "default": "freebayes",
                    "description": "Variant calling tool to use",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true,
                    "enum": ["bcftools", "gatk", "freebayes"]
                },
                "calling_params": {
                    "type": "string",
                    "description": "Extra variant caller options in quotes",
                    "help": "Useful if you would like to fine tune your variant calling analysis.",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "suspect": {
                    "type": "boolean",
                    "default": false,
                    "description": "Use the suspect suite of tools to add ML predictions",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "no_flagstat": {
                    "type": "boolean",
                    "default": false,
                    "description": "Don't collect flagstats",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "no_delly": {
                    "type": "boolean",
                    "default": false,
                    "description": "Don't run delly",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "tbprofiler_opts": {
                    "type": "string",
                    "description": "Extra options in quotes for TBProfiler",
                    "fa_icon": "fas fa-italic",
                    "hidden": false
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/tbprofiler_parameters"
        }
    ]
}
