{
    "params": {
        "fasta": {
            "type": "file",
            "description": "Path to input FASTA file(s) containing immune protein sequences",
            "default": "s3://omic/eureka/immunebuilder/antibody_test.fasta",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.fasta",
            "examples": [
                "s3://omic/eureka/immunebuilder/antibody.fasta",
                "s3://omic/eureka/immunebuilder/*.fasta"
            ],
            "pattern": ".*\\.(fasta|fa|faa)$",
            "enum": [],
            "validation": {},
            "notes": "FASTA format requirements vary by mode. Antibody: >H (heavy chain) and >L (light chain). Nanobody: >H (heavy chain only). TCR: >A (alpha chain) and >B (beta chain)."
        },
        "outdir": {
            "type": "folder",
            "description": "Directory for ImmuneBuilder prediction output files",
            "default": "s3://omic/eureka/immunebuilder/output",
            "required": true,
            "pipeline_io": "output",
            "var_name": "params.outdir",
            "examples": [
                "s3://omic/eureka/immunebuilder/output",
                "s3://omic/eureka/immunebuilder/custom_output"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Directory where predicted PDB structures and log files will be stored. Will be created if it doesn't exist."
        },
        "mode": {
            "type": "string",
            "description": "Prediction mode specifying the type of immune protein",
            "default": "antibody",
            "required": true,
            "pipeline_io": "parameter",
            "var_name": "params.mode",
            "examples": [
                "antibody",
                "nanobody",
                "tcr"
            ],
            "pattern": "^(antibody|nanobody|tcr)$",
            "enum": ["antibody", "nanobody", "tcr"],
            "validation": {},
            "notes": "Determines which predictor to use: 'antibody' for ABodyBuilder2, 'nanobody' for NanoBodyBuilder2, 'tcr' for TCRBuilder2."
        },
        "verbose": {
            "type": "boolean",
            "description": "Enable verbose output during prediction",
            "default": true,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.verbose",
            "examples": [
                true,
                false
            ],
            "enum": [true, false],
            "validation": {},
            "notes": "When enabled, provides detailed progress information during structure prediction."
        },
        "original_weights": {
            "type": "boolean",
            "description": "Use original TCRBuilder2 weights instead of TCRBuilder2+ weights",
            "default": false,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.original_weights",
            "examples": [
                true,
                false
            ],
            "enum": [true, false],
            "validation": {},
            "notes": "Only applicable when mode is 'tcr'. By default, TCRBuilder2+ weights are used. Set to true to use the original TCRBuilder2 weights."
        }
    }
}