From 8dd0ef8d6ab60b2c66ea0a9deef4dd0b36474fd7 Mon Sep 17 00:00:00 2001
From: Olamide Isreal <olamide@omicmd.com>
Date: Tue, 24 Mar 2026 21:03:07 +0100
Subject: [PATCH] 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         | 13 +++++++------
 nextflow.config | 30 +++++++++++++++---------------
 params.json     | 18 +++++++++---------
 3 files changed, 31 insertions(+), 30 deletions(-)

diff --git a/main.nf b/main.nf
index c11293d..26ec68a 100644
--- a/main.nf
+++ b/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
diff --git a/nextflow.config b/nextflow.config
index bdf4600..c89b5a2 100644
--- a/nextflow.config
+++ b/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 {
-    $local {
-        cpus = 2
-        memory = '4 GB'
-    }
-}
diff --git a/params.json b/params.json
index aed0259..2f2d90f 100644
--- a/params.json
+++ b/params.json
@@ -2,30 +2,30 @@
     "params": {
         "pdb": {
             "type": "file",
-            "description": "Path pattern to PDB files for pKa prediction",
-            "default": "/mnt/OmicNAS/private/old/olamide/propka/input/1HPX.pdb",
+            "description": "Path to input PDB file for pKa prediction",
+            "default": "s3://omic/eureka/propka/1HPX.pdb",
             "required": true,
             "pipeline_io": "input",
             "var_name": "params.pdb",
             "examples": [
-                "/mnt/OmicNAS/private/old/olamide/propka/input/protein.pdb",
-                "/mnt/OmicNAS/private/old/olamide/propka/input/*.pdb"
+                "s3://omic/eureka/propka/1HPX.pdb",
+                "s3://omic/eureka/propka/protein.pdb"
             ],
             "pattern": ".*\\.pdb$",
             "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": [],