Configure propka pipeline for WES/k8s execution

- Update container reference to harbor.cluster.omic.ai/omic/propka:latest
- Add k8s profile to nextflow.config matching reference tool pattern
- Update params.json with s3://omic/eureka/propka/ paths
- Add stageInMode 'copy' to process definition
- Set params defaults to null for WES compatibility

params.json

@@ -2,30 +2,30 @@
     "params": {
         "pdb": {
             "type": "file",
-            "description": "Path pattern to PDB files for pKa prediction",
-            "default": "/mnt/OmicNAS/private/old/olamide/propka/input/1HPX.pdb",
+            "description": "Path to input PDB file for pKa prediction",
+            "default": "s3://omic/eureka/propka/1HPX.pdb",
             "required": true,
             "pipeline_io": "input",
             "var_name": "params.pdb",
             "examples": [
-                "/mnt/OmicNAS/private/old/olamide/propka/input/protein.pdb",
-                "/mnt/OmicNAS/private/old/olamide/propka/input/*.pdb"
+                "s3://omic/eureka/propka/1HPX.pdb",
+                "s3://omic/eureka/propka/protein.pdb"
             ],
             "pattern": ".*\\.pdb$",
             "enum": [],
             "validation": {},
-            "notes": "Can be a single PDB file or a pattern to match multiple PDB files."
+            "notes": "PDB file containing the protein structure for pKa prediction. Files should be in standard PDB format."
         },
         "outdir": {
             "type": "folder",
-            "description": "Directory for PROPKA prediction results",
-            "default": "/mnt/OmicNAS/private/old/olamide/propka/output",
+            "description": "Output directory for PROPKA prediction results",
+            "default": "s3://omic/eureka/propka/output",
             "required": true,
             "pipeline_io": "output",
             "var_name": "params.outdir",
             "examples": [
-                "/mnt/OmicNAS/private/old/olamide/propka/output",
-                "/path/to/custom/output"
+                "s3://omic/eureka/propka/output",
+                "s3://omic/eureka/propka/results"
             ],
             "pattern": ".*",
             "enum": [],