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

nextflow.config

@@ -1,7 +1,7 @@
 // Manifest for Nextflow metadata
 manifest {
     name = 'PROPKA-Nextflow'
-    author = 'Generated from PROPKA repository'
+    author = 'Olamide'
     homePage = 'https://github.com/jensengroup/propka'
     description = 'Nextflow pipeline for PROPKA - Empirical pKa prediction for proteins and protein-ligand complexes'
     mainScript = 'main.nf'
@@ -10,16 +10,24 @@ manifest {
 
 // Global default parameters
 params {
-    pdb = "/mnt/OmicNAS/private/old/olamide/propka/input/1HPX.pdb"
-    outdir = "/mnt/OmicNAS/private/old/olamide/propka/output"
+    pdb = null
+    outdir = null
     ph = 7.0
     options = ""
 }
 
-// Container configurations
-docker {
-    enabled = true
-    runOptions = ''
+profiles {
+    standard {
+        docker {
+            enabled = true
+            runOptions = '--rm'
+        }
+    }
+    k8s {
+        process {
+            container = 'harbor.cluster.omic.ai/omic/propka:latest'
+        }
+    }
 }
 
 // Process configurations
@@ -27,11 +35,3 @@ process {
     cpus = 1
     memory = '4 GB'
 }
-
-// Execution configurations
-executor {
-    $local {
-        cpus = 2
-        memory = '4 GB'
-    }
-}