{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/panaroo/run/params.json",
    "title": "Panaroo Module",
    "description": "A module for pangenome investigation",
    "type": "object",
    "definitions": {
        "panaroo_parameters": {
            "title": "Panaroo Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "use_panaroo": {
                    "type": "boolean",
                    "default": false,
                    "description": "Use Panaroo instead of PIRATE in the 'pangenome' subworkflow",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "panaroo_mode": {
                    "type": "string",
                    "default": "strict",
                    "description": "The stringency mode at which to run panaroo",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "enum": [
                        "strict",
                        "moderate",
                        "sensitive"
                    ],
                    "hidden": true
                },
                "panaroo_alignment": {
                    "type": "string",
                    "default": "core",
                    "description": "Output alignments of core genes or all genes",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "enum": [
                        "core",
                        "pan"
                    ],
                    "hidden": true
                },
                "panaroo_aligner": {
                    "type": "string",
                    "default": "mafft",
                    "description": "Aligner to use for core/pan genome alignment",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "enum": [
                        "mafft",
                        "prank",
                        "clustal"
                    ],
                    "hidden": true
                },
                "panaroo_core_threshold": {
                    "type": "number",
                    "default": 0.95,
                    "description": "Core-genome sample threshold",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "panaroo_threshold": {
                    "type": "number",
                    "default": 0.98,
                    "description": "Sequence identity threshold",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "panaroo_family_threshold": {
                    "type": "number",
                    "default": 0.7,
                    "description": "Protein family sequence identity threshold",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "len_dif_percent": {
                    "type": "number",
                    "default": 0.98,
                    "description": "Length difference cutoff",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "merge_paralogs": {
                    "type": "boolean",
                    "default": false,
                    "description": "Do not split paralogs",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "panaroo_opts": {
                    "type": "string",
                    "default": "",
                    "description": "Additional options to pass to panaroo",
                    "fa_icon": "fas fa-expand-arrows-alt"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/panaroo_parameters"
        }
    ]
}
