{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/ariba/run/params.json",
    "title": "Ariba Run Module",
    "description": "A module for gene identification through local assemblies",
    "type": "object",
    "definitions": {
        "ariba_run_parameters": {
            "title": "Ariba Run Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fa-solid fa-toolbox",
            "properties": {
                "ariba_db": {
                    "type": "string",
                    "description": "A database to query, if unavailable it will be downloaded to the path given by --datasets_cache",
                    "default": "",
                    "fa_icon": "fas fa-italic",
                    "enum": [
                        "argannot",
                        "card",
                        "ncbi",
                        "megares",
                        "plasmidfinder",
                        "resfinder",
                        "srst2_argannot",
                        "vfdb_core",
                        "vfdb_full",
                        "virulencefinder"
                    ],
                    "is_required": true
                },
                "nucmer_min_id": {
                    "type": "integer",
                    "description": "Minimum alignment identity (delta-filter -i)",
                    "default": 90,
                    "fa_icon": "fas fa-angle-double-down"
                },
                "nucmer_min_len": {
                    "type": "integer",
                    "description": "Minimum alignment identity (delta-filter -i)",
                    "default": 20,
                    "fa_icon": "fas fa-angle-double-down"
                },
                "nucmer_breaklen": {
                    "type": "integer",
                    "description": "Value to use for -breaklen when running nucmer",
                    "default": 200,
                    "fa_icon": "fas fa-hashtag",
                    "hidden": true
                },
                "assembly_cov": {
                    "type": "integer",
                    "description": "Target read coverage when sampling reads for assembly",
                    "default": 50,
                    "fa_icon": "fas fa-hashtag"
                },
                "min_scaff_depth": {
                    "type": "integer",
                    "description": "Minimum number of read pairs needed as evidence for scaffold link between two contigs",
                    "default": 10,
                    "fa_icon": "fas fa-angle-double-down",
                    "hidden": true
                },
                "spades_options": {
                    "type": "string",
                    "description": "Extra options to pass to Spades assembler",
                    "fa_icon": "fas fa-italic",
                    "hidden": true
                },
                "assembled_threshold": {
                    "type": "number",
                    "description": "If proportion of gene assembled (regardless of into how many contigs) is at least this value then the flag gene_assembled is set",
                    "default": 0.95,
                    "fa_icon": "fas fa-angle-double-down",
                    "hidden": true
                },
                "gene_nt_extend": {
                    "type": "integer",
                    "description": "Max number of nucleotides to extend ends of gene matches to look for start/stop codons",
                    "default": 30,
                    "fa_icon": "fas fa-angle-double-up",
                    "hidden": true
                },
                "unique_threshold": {
                    "type": "number",
                    "description": "If proportion of bases in gene assembled more than once is <= this value, then the flag unique_contig is set",
                    "default": 0.03,
                    "fa_icon": "fas fa-angle-double-down",
                    "hidden": true
                },
                "ariba_no_clean": {
                    "type": "boolean",
                    "description": "Do not clean up intermediate files created by Ariba.",
                    "fa_icon": "fas fa-fast-forward",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/ariba_run_parameters"
        }
    ]
}
