From 3bd8e954e1356fb45be3d74c0f66939d83e61210 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Fri, 2 Feb 2024 08:54:16 -0800
Subject: [PATCH] Set working directory for GLNexus docker

---
 .../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 818aa39c5..34e2a9b16 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java
@@ -244,6 +244,7 @@ public void execute(List<File> inputGvcfs, File outputVcf, PipelineOutputTracker
                 writer.println("sudo $DOCKER run --rm=true \\");
                 writer.println("\t-v \"${WD}:/work\" \\");
                 writer.println("\t-v \"${HOME}:/homeDir\" \\");
+                writer.println("\t -w /work \\");
                 if (!StringUtils.isEmpty(System.getenv("TMPDIR")))
                 {
                     writer.println("\t-v \"${TMPDIR}:/tmp\" \\");