Add WES pipeline configuration for pocketminer

- Add Nextflow pipeline (main.nf) with Harbor container image
- Add nextflow.config with k8s/k8s_gpu/standard profiles
- Add params.json for TRS/WES parameter discovery
- Add Dockerfile, entrypoint.py, meta.yml from original implementation
- Update paths to use /omic/eureka/Pocketminer/ convention
- Update .gitignore to allow params.json

meta.yml

@@ -0,0 +1,42 @@
+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