{
    "params": {
        "pdb": {
            "type": "file",
            "description": "Path to input PDB file for cryptic pocket prediction",
            "default": "s3://omic/eureka/Pocketminer/1HSG.pdb",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.pdb",
            "examples": [
                "s3://omic/eureka/Pocketminer/1HSG.pdb",
                "s3://omic/eureka/Pocketminer/protein.pdb"
            ],
            "pattern": ".*\\.pdb$",
            "enum": [],
            "validation": {},
            "notes": "PDB file containing the protein structure for cryptic binding pocket prediction."
        },
        "outdir": {
            "type": "folder",
            "description": "Output directory for PocketMiner prediction results",
            "default": "s3://omic/eureka/Pocketminer/output",
            "required": true,
            "pipeline_io": "output",
            "var_name": "params.outdir",
            "examples": [
                "s3://omic/eureka/Pocketminer/output",
                "s3://omic/eureka/Pocketminer/results"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Directory where prediction results (numpy arrays, text predictions, and JSON summary) will be stored."
        },
        "debug": {
            "type": "boolean",
            "description": "Save debug features (X, S, mask arrays)",
            "default": false,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.debug",
            "examples": [
                false,
                true
            ],
            "enum": [true, false],
            "validation": {},
            "notes": "Enable to save intermediate feature arrays for debugging purposes."
        }
    }
}