schema_input.json

{
    "$schema": "https://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/phac-nml/gasnomenclature/main/assets/schema_input.json",
    "title": "phac-nml/gasnomenclature 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'"
            },
            "address": {
                "type": "string",
                "pattern": "^\\d+(\\.\\d+)*$",
                "meta": ["address"],
                "description": "The loci-based typing identifier (address) of the sample",
                "error_message": "Invalid loci-based typing identifier. Please ensure that the address follows the correct format, consisting of one or more digits separated by periods. Example of a valid identifier: '1.1.1'. Please review and correct the entry"
            }
        },
        "required": ["sample", "mlst_alleles"]
    }
}