{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/seqsero2/params.json",
    "title": "SeqSero2 Module",
    "description": "A module for Salmonella serotype prediction",
    "type": "object",
    "definitions": {
        "seqsero2_parameters": {
            "title": "SeqSero2 Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "run_mode": {
                    "type": "string",
                    "default": "k",
                    "description": "Workflow to run. 'a' allele mode, or 'k' k-mer mode",
                    "enum": ["a", "k"],
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "input_type": {
                    "type": "string",
                    "default": "assembly",
                    "description": "Input format to analyze. 'assembly' or 'fastq'",
                    "enum": ["assembly", "fastq"],
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "bwa_mode": {
                    "type": "string",
                    "default": "mem",
                    "description": "Algorithms for bwa mapping for allele mode",
                    "enum": ["mem", "sam"],
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/seqsero2_parameters"
        }
    ]
}
