Bugfix to DeepVariant docker command

BimberLab · Jan 20, 2024 · 3d7f838 · 3d7f838
1 parent 8ea5625
commit 3d7f838
Showing 1 changed file with 7 additions and 0 deletions.
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java
@@ -264,6 +264,13 @@ public void execute(File inputBam, File refFasta, File outputGvcf, PipelineOutpu
             {
                 throw new PipelineJobException(e);
             }
+
+            execute(Arrays.asList("/bin/bash/", localBashScript.getPath()));
+
+            if (!outputGvcf.exists())
+            {
+                throw new PipelineJobException("File not found: " + outputGvcf.getPath());
+            }
         }
     }
 }