diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/DockerWrapper.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/DockerWrapper.java
index 3a61bf728..16c526909 100644
--- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/DockerWrapper.java
+++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/DockerWrapper.java
@@ -108,6 +108,7 @@ public void executeWithDocker(List<String> containerArgs, File workDir, Pipeline
             }
 
             writer.println("$DOCKER run --rm=true \\");
+            writer.println("\t--group-add keep-groups \\");
             if (_useLocalContainerStorage)
             {
                 getLogger().debug("Using local container storage: " + getLocalContainerDir().getPath());