From 262b7031d2164fcb338b2484abba07abff54911f Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Fri, 2 Feb 2024 08:54:53 -0800
Subject: [PATCH] Add GLnexus.DB as intermediate file

---
 .../src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java | 1 +
 1 file changed, 1 insertion(+)

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java
index 34e2a9b16..547ac2bd3 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java
@@ -284,6 +284,7 @@ public void execute(List<File> inputGvcfs, File outputVcf, PipelineOutputTracker
 
                 // Command will fail if this exists:
                 File dbDir = new File (outputVcf.getParentFile(), "GLnexus.DB");
+                tracker.addIntermediateFile(dbDir);
                 if (dbDir.exists())
                 {
                     getLogger().debug("Deleting pre-existing GLnexus.DB dir");