From 5465d9b8b1fd018a8bb720d6d2d2ddac21c96d96 Mon Sep 17 00:00:00 2001
From: Olamide Isreal <olamide@omicmd.com>
Date: Mon, 23 Mar 2026 13:51:38 +0100
Subject: [PATCH] Fix nextflow.config to match WES k8s pattern

- Match p2rank's working config structure: k8s profile only sets container
- Let WES-generated profile.config handle executor, storage, and k8s settings
- Add memory (8GB) and cpu (2) resource requests
- Set params defaults to null (values provided by WES experiment_params)
- Add manifest metadata
---
 main.nf         |  4 ++--
 nextflow.config | 50 ++++++++++++++++++++++++-------------------------
 2 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/main.nf b/main.nf
index a7bfe58..2303773 100644
--- a/main.nf
+++ b/main.nf
@@ -3,8 +3,8 @@
 nextflow.enable.dsl=2
 
 // Parameters
-params.pdb = '/omic/eureka/Pocketminer/1HSG.pdb'
-params.outdir = '/omic/eureka/Pocketminer/output'
+params.pdb = null
+params.outdir = null
 params.model_path = '/workspace/gvp/models/pocketminer'
 params.debug = false
 
diff --git a/nextflow.config b/nextflow.config
index 065a56f..d3ab26c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,36 +1,36 @@
+// Manifest for Nextflow metadata
+manifest {
+    name = 'pocketminer-Nextflow'
+    author = 'Olamide'
+    homePage = 'https://github.com/Mickdub/gvp'
+    description = 'Nextflow pipeline for PocketMiner - cryptic binding pocket prediction using geometric deep learning'
+    mainScript = 'main.nf'
+    version = '1.0.0'
+}
+
+// Global default parameters
+params {
+    pdb = null
+    outdir = null
+    debug = false
+}
+
 profiles {
     standard {
         docker {
             enabled = true
-            temp = 'auto'
+            runOptions = '--rm'
         }
     }
-
     k8s {
         process {
-            executor = 'k8s'
-        }
-        docker {
-            enabled = true
-        }
-        k8s {
-            storageClaimName = 'eureka-pvc'
-            storageMountPath = '/omic/eureka'
-        }
-    }
-
-    k8s_gpu {
-        process {
-            executor = 'k8s'
-            pod = [[nodeSelector: 'nvidia.com/gpu.present=true']]
-            accelerator = [request: 1, type: 'nvidia.com/gpu']
-        }
-        docker {
-            enabled = true
-        }
-        k8s {
-            storageClaimName = 'eureka-pvc'
-            storageMountPath = '/omic/eureka'
+            container = 'harbor.cluster.omic.ai/omic/pocketminer:latest'
         }
     }
 }
+
+// Process configurations
+process {
+    cpus = 2
+    memory = '8 GB'
+}