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

@@ -2,14 +2,15 @@
 
 nextflow.enable.dsl=2
 
-params.pdb = "/mnt/OmicNAS/private/old/olamide/propka/input/1HPX.pdb"
+params.pdb = null
-params.outdir = "/mnt/OmicNAS/private/old/olamide/propka/output"
+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

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"
+    pdb = null
-    outdir = "/mnt/OmicNAS/private/old/olamide/propka/output"
+    outdir = null
     ph = 7.0
     options = ""
 }
 
-// Container configurations
+profiles {
+    standard {
         docker {
             enabled = true
-    runOptions = ''
+            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'
-    }
-}

params.json

@@ -2,30 +2,30 @@
     "params": {
         "pdb": {
             "type": "file",
-            "description": "Path pattern to PDB files for pKa prediction",
+            "description": "Path to input PDB file for pKa prediction",
-            "default": "/mnt/OmicNAS/private/old/olamide/propka/input/1HPX.pdb",
+            "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",
+                "s3://omic/eureka/propka/1HPX.pdb",
-                "/mnt/OmicNAS/private/old/olamide/propka/input/*.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",
+            "description": "Output directory for PROPKA prediction results",
-            "default": "/mnt/OmicNAS/private/old/olamide/propka/output",
+            "default": "s3://omic/eureka/propka/output",
             "required": true,
             "pipeline_io": "output",
             "var_name": "params.outdir",
             "examples": [
-                "/mnt/OmicNAS/private/old/olamide/propka/output",
+                "s3://omic/eureka/propka/output",
-                "/path/to/custom/output"
+                "s3://omic/eureka/propka/results"
             ],
             "pattern": ".*",
             "enum": [],