{
    "params": {
        "TPM": {
            "type": "file",
            "description": "Path to TPM (Transcripts Per Million) CSV file",
            "default": "s3://omic/eureka/corto/20002_1289_female_patient_0_TPM.csv",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.TPM",
            "examples": [
                "s3://omic/eureka/corto/20002_1289_female_patient_0_TPM.csv"
            ],
            "pattern": ".*\\.csv$",
            "enum": [],
            "validation": {},
            "notes": "A CSV file containing TPM values with ENSG IDs as rows and samples as columns"
        },
        "regulon": {
            "type": "file",
            "description": "Path to regulon RDA file",
            "default": "s3://omic/eureka/corto/regulon.rda",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.regulon",
            "examples": [
                "s3://omic/eureka/corto/regulon.rda"
            ],
            "pattern": ".*\\.rda$",
            "enum": [],
            "validation": {},
            "notes": "An R data file containing regulon information for the CORTO analysis"
        },
        "outdir": {
            "type": "folder",
            "description": "Directory for CORTO analysis results",
            "default": "s3://omic/eureka/corto/output",
            "required": true,
            "pipeline_io": "output",
            "var_name": "params.outdir",
            "examples": [
                "s3://omic/eureka/corto/output"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Directory where metabolome prediction results will be stored"
        }
    }
}