{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/checkm/lineagewf/params.json",
    "title": "CheckM Module",
    "description": "A module to assess the assembly quality of your samples",
    "type": "object",
    "definitions": {
        "checkm_parameters": {
            "title": "CheckM Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fa-solid fa-toolbox",
            "properties": {
                "checkm_unique": {
                    "type": "integer",
                    "description": "Minimum number of unique phylogenetic markers required to use lineage-specific marker set.",
                    "default": 10,
                    "fa_icon": "fas fa-angle-double-down"
                },
                "checkm_multi": {
                    "type": "integer",
                    "description": "Maximum number of multi-copy phylogenetic markers before defaulting to domain-level marker set.",
                    "default": 10,
                    "fa_icon": "fas fa-angle-double-up"
                },
                "aai_strain": {
                    "type": "number",
                    "description": "AAI threshold used to identify strain heterogeneity",
                    "default": 0.9,
                    "fa_icon": "fas fa-hashtag"
                },
                "checkm_length": {
                    "type": "number",
                    "description": "Percent overlap between target and query",
                    "default": 0.7,
                    "fa_icon": "fas fa-hashtag"
                },
                "full_tree": {
                    "type": "boolean",
                    "description": "Use the full tree (requires ~40GB of memory) for determining lineage of each bin.",
                    "fa_icon": "fas fa-tree",
                    "hidden": true
                },
                "skip_pseudogene_correction": {
                    "type": "boolean",
                    "description": "Skip identification and filtering of pseudogene",
                    "fa_icon": "fas fa-fast-forward",
                    "hidden": true
                },
                "ignore_thresholds": {
                    "type": "boolean",
                    "description": "Ignore model-specific score thresholds",
                    "fa_icon": "fas fa-eye-slash",
                    "hidden": true
                },
                "checkm_ali": {
                    "type": "boolean",
                    "description": "Generate HMMER alignment file for each bin",
                    "fa_icon": "fas fa-hard-hat",
                    "hidden": true
                },
                "checkm_nt": {
                    "type": "boolean",
                    "description": "Generate nucleotide gene sequences for each bin",
                    "fa_icon": "fas fa-hard-hat",
                    "hidden": true
                },
                "force_domain": {
                    "type": "boolean",
                    "description": "Use domain-level sets for all bins",
                    "fa_icon": "fas fa-hammer",
                    "hidden": true
                },
                "no_refinement": {
                    "type": "boolean",
                    "description": "Do not perform lineage-specific marker set refinement",
                    "fa_icon": "fas fa-fast-forward",
                    "hidden": true
                },
                "individual_markers": {
                    "type": "boolean",
                    "description": "Treat marker as independent",
                    "fa_icon": "fas fa-check",
                    "hidden": true
                },
                "skip_adj_correction": {
                    "type": "boolean",
                    "description": "Do not exclude adjacent marker genes when estimating contamination",
                    "fa_icon": "fas fa-fast-forward",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/checkm_parameters"
        }
    ]
}
