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

@@ -1,15 +1,18 @@
-aws {
+docker {
-    client {
+    enabled = true
-        endpoint = 'https://s3.cluster.omic.ai'
-        s3PathStyleAccess = 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'