From 7c8629330bb0d1c3a8418fba7ea65c5aec8daa13 Mon Sep 17 00:00:00 2001
From: Olamide Isreal <olamide@omicmd.com>
Date: Mon, 16 Mar 2026 15:42:33 +0100
Subject: [PATCH] Add global docker/process config and fix k8s_gpu profile

- Enable docker globally (required by WES)
- Set default container, memory (32GB), cpus (4) at process level
- Add NVIDIA_VISIBLE_DEVICES env for GPU visibility in k8s_gpu

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 nextflow.config | 23 ++++++++++-------------
 1 file changed, 10 insertions(+), 13 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 0b444fa..c62638d 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,15 +1,18 @@
-aws {
-    client {
-        endpoint = 'https://s3.cluster.omic.ai'
-        s3PathStyleAccess = true
-    }
+docker {
+    enabled = true
+}
+
+process {
+    container = 'harbor.cluster.omic.ai/omic/chai1:latest'
+    memory = '32 GB'
+    cpus = 4
 }
 
 profiles {
     standard {
         docker {
-            enabled = true
             temp = 'auto'
+            runOptions = '--gpus all'
         }
     }
 
@@ -17,9 +20,6 @@ profiles {
         process {
             executor = 'k8s'
         }
-        docker {
-            enabled = true
-        }
         k8s {
             storageClaimName = 'eureka-pvc'
             storageMountPath = '/omic/eureka'
@@ -31,12 +31,9 @@ profiles {
     k8s_gpu {
         process {
             executor = 'k8s'
-            pod = [[nodeSelector: 'nvidia.com/gpu.present=true']]
+            pod = [[nodeSelector: 'nvidia.com/gpu.present=true'], [env: 'NVIDIA_VISIBLE_DEVICES', value: 'all']]
             accelerator = [request: 1, type: 'nvidia.com/gpu']
         }
-        docker {
-            enabled = true
-        }
         k8s {
             storageClaimName = 'eureka-pvc'
             storageMountPath = '/omic/eureka'