From b099a5ee383583b7059f8968b9289c501e6bfab7 Mon Sep 17 00:00:00 2001
From: Olamide Isreal <olamide@omicmd.com>
Date: Wed, 18 Mar 2026 11:56:19 +0100
Subject: [PATCH] Update nextflow config for Wes K8s execution with proper
 profiles

Add standard, k8s, and k8s_gpu profiles matching reference tool patterns.
Configure PVC mounting for eureka storage and GPU node selection.
Remove Docker-specific containerOptions from process definition.
---
 main.nf         |  1 -
 nextflow.config | 64 ++++++++++++++++++++++++++++++-------------------
 2 files changed, 39 insertions(+), 26 deletions(-)

diff --git a/main.nf b/main.nf
index 6d93628..05f6d89 100644
--- a/main.nf
+++ b/main.nf
@@ -25,7 +25,6 @@ params.weights = '/mnt/databases/RFAA_paper_weights.pt'
 
 process RFAA_PREDICT {
     container 'harbor.cluster.omic.ai/omic/rosettafold-all-atom:latest'
-    containerOptions '--rm --gpus all -v /mnt:/mnt'
     publishDir params.outdir, mode: 'copy'
     stageInMode 'copy'
 
diff --git a/nextflow.config b/nextflow.config
index 6e54507..7e81c60 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -32,10 +32,45 @@ params {
     weights = "/mnt/databases/RFAA_paper_weights.pt"
 }
 
-// Container configurations
-docker {
-    enabled = true
-    runOptions = '--gpus all'
+// Profiles
+profiles {
+    standard {
+        docker {
+            enabled = true
+            temp = 'auto'
+            runOptions = '--gpus all -v /mnt:/mnt'
+        }
+    }
+
+    k8s {
+        process {
+            executor = 'k8s'
+            container = 'harbor.cluster.omic.ai/omic/rosettafold-all-atom:latest'
+        }
+        docker {
+            enabled = true
+        }
+        k8s {
+            storageClaimName = 'eureka-pvc'
+            storageMountPath = '/omic/eureka'
+        }
+    }
+
+    k8s_gpu {
+        process {
+            executor = 'k8s'
+            container = 'harbor.cluster.omic.ai/omic/rosettafold-all-atom:latest'
+            pod = [[nodeSelector: 'nvidia.com/gpu.present=true']]
+            accelerator = [request: 1, type: 'nvidia.com/gpu']
+        }
+        docker {
+            enabled = true
+        }
+        k8s {
+            storageClaimName = 'eureka-pvc'
+            storageMountPath = '/omic/eureka'
+        }
+    }
 }
 
 // Process configurations
@@ -43,24 +78,3 @@ process {
     cpus = 8
     memory = '64 GB'
 }
-
-// Execution configurations
-executor {
-    $local {
-        cpus = 16
-        memory = '64 GB'
-    }
-}
-
-// Profiles
-profiles {
-    k8s {
-        process {
-            container = 'harbor.cluster.omic.ai/omic/rosettafold-all-atom:latest'
-        }
-        docker {
-            enabled = true
-            runOptions = '--gpus all'
-        }
-    }
-}