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\" \\");