{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/stecfinder/params.json",
    "title": "STECFinder Module",
    "description": "A module to serotyping shigella toxin producing E. coli (STEC)",
    "type": "object",
    "definitions": {
        "stecfinder_parameters": {
            "title": "STECFinder Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "stecfinder_use_reads": {
                    "type": "boolean",
                    "default": false,
                    "description": "Paired-end Illumina reads will be used instead of assemblies",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "stecfinder_hits": {
                    "type": "boolean",
                    "default": false,
                    "description": "Show detailed gene search results",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "stecfinder_cutoff": {
                    "type": "number",
                    "default": 10.0,
                    "description": "Minimum read coverage for gene to be called",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "stecfinder_length": {
                    "type": "number",
                    "default": 50.0,
                    "description": "Percentage of gene length needed for positive call",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "stecfinder_ipah_length": {
                    "type": "number",
                    "default": 10.0,
                    "description": "Percentage of ipaH gene length needed for positive gene call",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "stecfinder_ipah_depth": {
                    "type": "number",
                    "default": 1.0,
                    "description": "Minimum depth for positive ipaH gene call (requires --stecfinder_use_reads)",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "stecfinder_stx_length": {
                    "type": "number",
                    "default": 10.0,
                    "description": "Percentage of stx gene length needed for positive gene call",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "stecfinder_stx_depth": {
                    "type": "number",
                    "default": 10.0,
                    "description": "Minimum depth for positive stx gene call (requires --stecfinder_use_reads)",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "stecfinder_o_length": {
                    "type": "number",
                    "default": 60.0,
                    "description": "Percentage of wz_ gene length needed for positive call",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "stecfinder_o_depth": {
                    "type": "number",
                    "default": 1.0,
                    "description": "Minimum depth for positive qz_ gene call (requires --stecfinder_use_reads)",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "stecfinder_h_length": {
                    "type": "number",
                    "default": 60.0,
                    "description": "Percentage of fliC gene length needed for positive call",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "stecfinder_h_depth": {
                    "type": "number",
                    "default": 1.0,
                    "description": "Minimum depth for positive fliC gene call (requires --stecfinder_use_reads)",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/stecfinder_parameters"
        }
    ]
}
