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

params.json

@@ -0,0 +1,51 @@
+{
+    "params": {
+        "pdb": {
+            "type": "file",
+            "description": "Path to input PDB file for cryptic pocket prediction",
+            "default": "s3://omic/eureka/Pocketminer/1HSG.pdb",
+            "required": true,
+            "pipeline_io": "input",
+            "var_name": "params.pdb",
+            "examples": [
+                "s3://omic/eureka/Pocketminer/1HSG.pdb",
+                "s3://omic/eureka/Pocketminer/protein.pdb"
+            ],
+            "pattern": ".*\\.pdb$",
+            "enum": [],
+            "validation": {},
+            "notes": "PDB file containing the protein structure for cryptic binding pocket prediction."
+        },
+        "outdir": {
+            "type": "folder",
+            "description": "Output directory for PocketMiner prediction results",
+            "default": "s3://omic/eureka/Pocketminer/output",
+            "required": true,
+            "pipeline_io": "output",
+            "var_name": "params.outdir",
+            "examples": [
+                "s3://omic/eureka/Pocketminer/output",
+                "s3://omic/eureka/Pocketminer/results"
+            ],
+            "pattern": ".*",
+            "enum": [],
+            "validation": {},
+            "notes": "Directory where prediction results (numpy arrays, text predictions, and JSON summary) will be stored."
+        },
+        "debug": {
+            "type": "boolean",
+            "description": "Save debug features (X, S, mask arrays)",
+            "default": false,
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.debug",
+            "examples": [
+                false,
+                true
+            ],
+            "enum": [true, false],
+            "validation": {},
+            "notes": "Enable to save intermediate feature arrays for debugging purposes."
+        }
+    }
+}