{
  "$schema": "http://json-schema.org/draft-07/schema",
  "$id": "https://raw.githubusercontent.com/pgscatalog/pgsc_calc/dev/assets/schemas/samplesheet.json",
  "title": "Target genome schema",
  "description": "Validates the JSON representation of a samplesheet",
  "type": "array",
  "uniqueItems": true,
  "minItems": 1,
  "items": {
    "type": "object",
    "properties": {
      "sampleset": {
        "type": "string",
        "pattern": "^[a-zA-Z0-9]*$",
        "description": "Sampleset name must be provided and cannot contain spaces or reserved characters ('_' or '.')"
      },
      "path": {
        "description": "A list of resolved target genome file paths",
        "type": "array",
        "uniqueItems": true,
        "minItems": 1,
        "maxItems": 3,
        "items": {
          "type": "string"
        }
      },
      "chrom": {
        "description": "Specify the chromosome of associated genotyping data (must be in {1-22, X, XY, Y}). If all chromosomes are in the associated file (e.g. your data is not split by chromosome), set to null.",
        "type": [
          "null",
          "string"
        ],
        "minLength": 1
      },
      "format": {
        "description": "Target genome data format.",
        "type": "string",
        "enum": [
          "pfile",
          "bfile",
          "vcf"
        ]
      },
      "vcf_genotype_field": {
        "description": "Specify whether to import genotypes (default: GT), or imputed dosages (DS) from the VCF file.",
        "type": "boolean"
      }
    },
    "required": [
      "sampleset",
      "path",
      "format",
      "chrom"
    ]
  }
}