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

main.nf

@@ -2,22 +2,23 @@
 
 nextflow.enable.dsl=2
 
-params.pdb = "/mnt/OmicNAS/private/old/olamide/propka/input/1HPX.pdb"
-params.outdir = "/mnt/OmicNAS/private/old/olamide/propka/output"
+params.pdb = null
+params.outdir = null
 params.ph = 7.0
 params.options = ""
 
 process PROPKA {
-    container 'propka:latest'
+    container 'harbor.cluster.omic.ai/omic/propka:latest'
     publishDir params.outdir, mode: 'copy'
-    
+    stageInMode 'copy'
+
     input:
         path pdb
-    
+
     output:
         path "${pdb.baseName}.pka", emit: pka_file
         path "run.log"
-    
+
     script:
         """
         propka3 ${params.options} --pH ${params.ph} ${pdb} 2>&1 | tee run.log