From 8bb6720fc10be94d9daca670e85b7e36b3fe8922 Mon Sep 17 00:00:00 2001
From: Olamide Isreal <olamide@omicmd.com>
Date: Mon, 16 Mar 2026 15:34:52 +0100
Subject: [PATCH] Add k8s and k8s_gpu profiles for WES execution

WES runs Nextflow with -profile k8s_gpu for GPU workloads.
Profiles configure K8s executor, GPU node selector, and
eureka-pvc storage claim for data access.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 nextflow.config | 46 +++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 41 insertions(+), 5 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 3770b88..0b444fa 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,11 +1,47 @@
-docker {
-    enabled = true
-    temp = 'auto'
-}
-
 aws {
     client {
         endpoint = 'https://s3.cluster.omic.ai'
         s3PathStyleAccess = true
     }
 }
+
+profiles {
+    standard {
+        docker {
+            enabled = true
+            temp = 'auto'
+        }
+    }
+
+    k8s {
+        process {
+            executor = 'k8s'
+        }
+        docker {
+            enabled = true
+        }
+        k8s {
+            storageClaimName = 'eureka-pvc'
+            storageMountPath = '/omic/eureka'
+            namespace = 'nextflow'
+            serviceAccount = 'nextflow'
+        }
+    }
+
+    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'
+            namespace = 'nextflow'
+            serviceAccount = 'nextflow'
+        }
+    }
+}