Fix executions hangs on finalisation exception (#5070)

Signed-off-by: Paolo Di Tommaso <[email protected]>
nextflow-io · Jul 9, 2024 · 4c207c2 · 4c207c2
1 parent e6a5e17
commit 4c207c2
Showing 1 changed file with 11 additions and 1 deletion.
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy
@@ -663,14 +663,24 @@ class TaskPollingMonitor implements TaskMonitor {
 
             // finalize the task asynchronously
             if( enableAsyncFinalizer ) {
-                finalizerPool.submit( ()-> finalizeTask(handler) )
+                finalizerPool.submit( ()-> safeFinalizeTask(handler) )
             }
             else {
                 finalizeTask(handler)
             }
         }
     }
 
+    protected void safeFinalizeTask(TaskHandler handler) {
+        try {
+            finalizeTask(handler)
+        }
+        catch (Throwable t) {
+            log.error "Unexpected error while finalizing task '${handler.task.name}' - cause: ${t.message}"
+            session.abort(t)
+        }
+    }
+
     protected void finalizeTask( TaskHandler handler ) {
         // finalize the task execution
         final fault = handler.task.processor.finalizeTask(handler.task)