{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/scoary/params.json",
    "title": "Scoary Module",
    "description": "A module conducting GWAS using pangenome outputs",
    "type": "object",
    "definitions": {
        "scoary_parameters": {
            "title": "Scoary Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "traits": {
                    "type": "string",
                    "description": "Input trait table (CSV) to test for associations",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "p_value_cutoff": {
                    "type": "number",
                    "default": 0.05,
                    "description": "For statistical tests, genes with higher p-values will not be reported",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "correction": {
                    "type": "string",
                    "default": "I",
                    "description": "Apply the indicated filtration measure.",
                    "help": "I=Individual (naive) p-value. B=Bonferroni adjusted p-value. BH=Benjamini-Hochberg adjusted p. PW=Best (lowest) pairwise comparison. EPW=Entire range of pairwise comparison p-values. P=Empirical p-value from permutations",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "enum": ["I", "B", "BH","PW","EPW","P"],
                    "hidden": true
                },
                "permute": {
                    "type": "integer",
                    "default": 0,
                    "description": "Perform N number of permutations of the significant results post-analysis",
                    "fa_icon": "fas fa-expand-arrows-alt"
                },
                "start_col": {
                    "type": "integer",
                    "default": 15,
                    "description": "On which column in the gene presence/absence file do individual strain info start",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/scoary_parameters"
        }
    ]
}
