{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/midas/species/params.json",
    "title": "Bactopia pipeline parameters",
    "description": "A module for determining the species abundance of a sample",
    "type": "object",
    "definitions": {
        "midas_species_parameters": {
            "title": "MIDAS species Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "midas_db": {
                    "type": "string",
                    "description": "A single tarball or path to a MIDAS formatted database",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "is_required": true
                },
                "midas_word_size": {
                    "type": "integer",
                    "description": "Word size for BLAST search",
                    "default": 28,
                    "fa_icon": "fas fa-angle-double-down"
                },
                "midas_aln_cov": {
                    "type": "number",
                    "description": "Discard reads with alignment coverage < ALN_COV",
                    "default": 0.75,
                    "fa_icon": "fas fa-angle-double-down"
                },
                "midas_opts": {
                    "type": "string",
                    "description": "Extra MIDAS options",
                    "fa_icon": "fas fa-italic"
                },
                "midas_debug": {
                    "type": "boolean",
                    "default": false,
                    "description": "Keep all temporary files created by MIDAS",
                    "fa_icon": "fas fa-italic"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/midas_species_parameters"
        }
    ]
}
