{
    "params": {
        "input_dir": {
            "type": "folder",
            "description": "Directory containing FASTA files and optional restraints",
            "default": "s3://omic/eureka/chai-lab/input",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.input_dir",
            "examples": [
                "s3://omic/eureka/chai-lab/input"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Directory containing FASTA files (with *_complex.fasta suffix) and optional restraints files (with *_restraints.txt suffix)"
        },
        "outdir": {
            "type": "folder",
            "description": "Directory for chai1 prediction results",
            "default": "s3://omic/eureka/chai-lab/output",
            "required": true,
            "pipeline_io": "output",
            "var_name": "params.outdir",
            "examples": [
                "s3://omic/eureka/chai-lab/output"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Directory where prediction results and log files will be stored. Will be created if it doesn't exist."
        },
        "use_msa": {
            "type": "boolean",
            "description": "Enable/disable MSA server usage",
            "default": true,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.use_msa",
            "examples": [
                true,
                false
            ],
            "enum": [true, false],
            "validation": {},
            "notes": "Whether to use MSA server for improved predictions"
        },
        "msa_server": {
            "type": "string",
            "description": "MSA server URL",
            "default": "https://api.colabfold.com",
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.msa_server",
            "examples": [
                "https://api.colabfold.com"
            ],
            "pattern": "^https?://.*",
            "enum": [],
            "validation": {},
            "notes": "URL of the MSA server to use when use_msa is enabled"
        },
        "num_samples": {
            "type": "integer",
            "description": "Number of diffusion samples to generate",
            "default": 5,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.num_samples",
            "examples": [
                5,
                10
            ],
            "pattern": "^[1-9]\\d*$",
            "enum": [],
            "validation": {
                "min": 1,
                "max": 50
            },
            "notes": "Number of structure samples to generate using diffusion"
        }
    }
}