From fafddb539fca8472a8c0d14611848863cb73192b Mon Sep 17 00:00:00 2001
From: thalassemia <cheah_sean@yahoo.com>
Date: Fri, 20 Sep 2024 19:00:11 -0700
Subject: [PATCH] Make Nextflow raise error if any job failure was ignored
 (requires Nextflow 24.05.0-edge)

---
 runscripts/nextflow/config.template | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/runscripts/nextflow/config.template b/runscripts/nextflow/config.template
index e8da845d0..86f6593c9 100644
--- a/runscripts/nextflow/config.template
+++ b/runscripts/nextflow/config.template
@@ -30,6 +30,7 @@ profiles {
         process.maxRetries = 1
         // Check Google Cloud latest spot pricing / performance
         process.machineType = 't2d-standard-1'
+        workflow.failOnIgnore = true
     }
     sherlock {
         process.memory = {
@@ -78,10 +79,12 @@ profiles {
         // Write out job status to log file less frequently
         // than we check queue status (log correct and latest status)
         executor.dumpInterval = '6 min'
+        workflow.failOnIgnore = true
     }
     standard {
         process.executor = 'local'
         params.projectRoot = "${launchDir}"
         params.publishDir = "PUBLISH_DIR"
+        workflow.failOnIgnore = true
     }
 }