Update gVCF index locator in GLNexus step

BimberLab · Jan 31, 2024 · 45d7f14 · 45d7f14
1 parent e3db53e
commit 45d7f14
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java
@@ -212,7 +212,7 @@ public void execute(List<File> inputGvcfs, File outputVcf, PipelineOutputTracker
             for (File f : inputGvcfs)
             {
                 gvcfsLocal.add(ensureLocalCopy(f, workDir, tracker));
-                ensureLocalCopy(SequenceUtil.getExpectedIndex(f), workDir, tracker);
+                ensureLocalCopy(new File(f.getPath() + ".tbi"), workDir, tracker);
             }
 
             File localBashScript = new File(workDir, "docker.sh");