Mark index folder for deletion

bbimber · bbimber · commit 655c47aff786 · 2025-05-20T13:02:20.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BBMapWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BBMapWrapper.java
@@ -101,6 +101,7 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
                 }
 
                 FileUtils.moveDirectory(localIdx, refDir);
+                output.addIntermediateFile(refDir);
             }
             catch (IOException e)
             {

Original file line number	Diff line number	Diff line change
`@@ -101,6 +101,7 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu`
`101`	`101`	`}`
`102`	`102`
`103`	`103`	`FileUtils.moveDirectory(localIdx, refDir);`
	`104`	`+ output.addIntermediateFile(refDir);`
`104`	`105`	`}`
`105`	`106`	`catch (IOException e)`
`106`	`107`	`{`