params:
  - outdir:
      type: file
      description: path where output files will be deposited
      required: true
  - model_path:
      type: file
      description: path to pre-trained PocketMiner model checkpoint
      default: /workspace/gvp/models/pocketminer
      required: false
  - debug:
      type: boolean
      description: save debug features (X, S, mask arrays)
      default: false
      required: false
input:
  - pdb:
      type: file
      description: PDB file path for protein structure
  - dynamics_optional:
      type: file
      description: optional MD trajectory or ensemble of conformers for enhanced cryptic pocket detection
      required: false
output:
  - predictions_npy:
      type: file
      description: NumPy binary file containing per-residue cryptic pocket scores
  - predictions_txt:
      type: file
      description: human-readable text file with per-residue cryptic pocket scores (4 decimal places)
  - summary:
      type: file
      description: JSON file containing overall cryptic pocket score, high/medium confidence residue counts, pocket clusters, and metadata
  - features_debug:
      type: file
      description: (optional) protein features array for debugging
  - sequence_debug:
      type: file
      description: (optional) sequence data array for debugging
  - mask_debug:
      type: file
      description: (optional) masking array for debugging