schema_input.json

{
    "$schema": "https://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/phac-nml/gasclustering/main/assets/schema_input.json",
    "title": "phac-nml/gasclustering pipeline - params.input schema",
    "description": "Schema for the file provided with params.input",
    "type": "array",
    "items": {
        "type": "object",
        "properties": {
            "sample": {
                "type": "string",
                "pattern": "^\\S+$",
                "meta": ["irida_id"],
                "unique": true,
                "errorMessage": "Sample name must be provided and cannot contain spaces."
            },
            "sample_name": {
                "type": "string",
                "meta": ["id"],
                "errorMessage": "Sample name is optional, if provided will replace sample for filenames and outputs"
            },
            "mlst_alleles": {
                "type": "string",
                "format": "file-path",
                "pattern": "^\\S+\\.mlst(\\.subtyping)?\\.json(\\.gz)?$",
                "errorMessage": "MLST JSON file from locidex report, cannot contain spaces and must have the extension: '.mlst.json', '.mlst.json.gz', '.mlst.subtyping.json', or 'mlst.subtyping.json.gz'"
            },
            "metadata_1": {
                "type": "string",
                "meta": ["metadata_1"],
                "errorMessage": "Metadata associated with the sample (metadata_1).",
                "default": "",
                "pattern": "^[^\\n\\t\"]+$"
            },
            "metadata_2": {
                "type": "string",
                "meta": ["metadata_2"],
                "errorMessage": "Metadata associated with the sample (metadata_2).",
                "default": "",
                "pattern": "^[^\\n\\t\"]+$"
            },
            "metadata_3": {
                "type": "string",
                "meta": ["metadata_3"],
                "errorMessage": "Metadata associated with the sample (metadata_3).",
                "default": "",
                "pattern": "^[^\\n\\t\"]+$"
            },
            "metadata_4": {
                "type": "string",
                "meta": ["metadata_4"],
                "errorMessage": "Metadata associated with the sample (metadata_4).",
                "default": "",
                "pattern": "^[^\\n\\t\"]+$"
            },
            "metadata_5": {
                "type": "string",
                "meta": ["metadata_5"],
                "errorMessage": "Metadata associated with the sample (metadata_5).",
                "default": "",
                "pattern": "^[^\\n\\t\"]+$"
            },
            "metadata_6": {
                "type": "string",
                "meta": ["metadata_6"],
                "errorMessage": "Metadata associated with the sample (metadata_6).",
                "default": "",
                "pattern": "^[^\\n\\t\"]+$"
            },
            "metadata_7": {
                "type": "string",
                "meta": ["metadata_7"],
                "errorMessage": "Metadata associated with the sample (metadata_7).",
                "default": "",
                "pattern": "^[^\\n\\t\"]+$"
            },
            "metadata_8": {
                "type": "string",
                "meta": ["metadata_8"],
                "errorMessage": "Metadata associated with the sample (metadata_8).",
                "default": "",
                "pattern": "^[^\\n\\t\"]+$"
            }
        },
        "required": ["sample", "mlst_alleles"]
    }
}