{
  "params": {
    "// GENERAL PARAMETERS": {},
    "outdir": {
      "type": "folder",
      "description": "Output directory for results",
      "default": "/mnt/OmicNAS/private/old/gabe/digital_trials",
      "required": true,
      "pipeline_io": "output",
      "var_name": "params.outdir",
      "examples": [
        "/mnt/OmicNAS/private/old/gabe/digital_trials",
        "/path/to/custom/output"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Directory where all pipeline results will be stored"
    },
    "project_name": {
      "type": "string",
      "description": "Project identifier",
      "default": "test",
      "required": true,
      "pipeline_io": "parameter",
      "var_name": "params.project_name",
      "examples": [
        "test",
        "production",
        "drug_metabolism_study"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Identifier for the digital trials project"
    },
    "containerOptions": {
      "type": "string",
      "description": "Container runtime options",
      "default": "--gpus all --rm -v /mnt:/mnt",
      "required": false,
      "pipeline_io": "parameter",
      "var_name": "params.containerOptions",
      "examples": [
        "--gpus all --rm -v /mnt:/mnt",
        "--rm -v /data:/data"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Docker container runtime options for GPU usage and volume mounts"
    },
    "// BIOTRANSFORMER PARAMETERS": {},
    "container_biotransformer": {
      "type": "string",
      "description": "BioTransformer container image",
      "default": "biotransformer:latest",
      "required": true,
      "pipeline_io": "parameter",
      "var_name": "params.container_biotransformer",
      "examples": [
        "biotransformer:latest",
        "biotransformer:v1.0"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Docker container image for BioTransformer module"
    },
    "ligands": {
      "type": "folder",
      "description": "Path to input ligands directory",
      "default": "/Workspace/next/registry/pipelines/digital_trials/input",
      "required": true,
      "pipeline_io": "input",
      "var_name": "params.ligands",
      "examples": [
        "/Workspace/next/registry/pipelines/digital_trials/input",
        "/path/to/ligands"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Directory containing CSV files with ligand data for metabolic transformation"
    },
    "mode": {
      "type": "string",
      "description": "BioTransformer operation mode",
      "default": "HUMAN",
      "required": true,
      "pipeline_io": "parameter",
      "var_name": "params.mode",
      "examples": [
        "HUMAN",
        "SUPER",
        "MASS",
        "ORDERED"
      ],
      "pattern": "^(HUMAN|SUPER|MASS|ORDERED)$",
      "enum": [
        "HUMAN",
        "SUPER",
        "MASS",
        "ORDERED"
      ],
      "validation": {},
      "notes": "IMPORTANT: Use HUMAN mode as it's the only fully implemented option that returns expected metabolism to the last step"
    },
    "// CONPLEX PARAMETERS": {},
    "container_conplex": {
      "type": "string",
      "description": "CONPLEX container image",
      "default": "conplex_dig_pat:latest",
      "required": true,
      "pipeline_io": "parameter",
      "var_name": "params.container_conplex",
      "examples": [
        "conplex_dig_pat:latest",
        "conplex_dig_pat:v1.0"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Docker container image for CONPLEX module"
    },
    "mutated_protein_fasta": {
      "type": "folder",
      "description": "Path to mutated protein FASTA files directory",
      "default": "/Workspace/next/registry/pipelines/digital_trials/input",
      "required": true,
      "pipeline_io": "input",
      "var_name": "params.mutated_protein_fasta",
      "examples": [
        "/Workspace/next/registry/pipelines/digital_trials/input",
        "/path/to/protein/fasta/files"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Directory containing FASTA files with mutated protein sequences"
    },
    "threshold": {
      "type": "number",
      "description": "Binding affinity threshold for interactions",
      "default": 0.7,
      "required": false,
      "pipeline_io": "parameter",
      "var_name": "params.threshold",
      "examples": [
        0.5,
        0.7,
        0.9
      ],
      "pattern": "^\\d+(\\.\\d+)?$",
      "validation": {
        "min": 0.0,
        "max": 1.0
      },
      "notes": "Threshold value for determining significant binding interactions"
    },
    "screening_batch_size": {
      "type": "integer",
      "description": "Batch size for virtual screening",
      "default": 100000,
      "required": false,
      "pipeline_io": "parameter",
      "var_name": "params.screening_batch_size",
      "examples": [
        10000,
        100000,
        1000000
      ],
      "pattern": "^\\d+$",
      "validation": {
        "min": 1
      },
      "notes": "Batch size for virtual screening (100k is ideal to optimize performance)"
    },
    "protein_network_threshold": {
      "type": "number",
      "description": "Threshold for protein network analysis",
      "default": 0.95,
      "required": false,
      "pipeline_io": "parameter",
      "var_name": "params.protein_network_threshold",
      "examples": [
        0.9,
        0.95,
        0.99
      ],
      "pattern": "^\\d+(\\.\\d+)?$",
      "validation": {
        "min": 0.0,
        "max": 1.0
      },
      "notes": "Threshold value for protein-protein interaction network construction"
    }
  }
}