SRA download needs to use addDeferredIntermediateFile()

bbimber · bbimber · commit 470319be51a8 · 2025-01-02T17:09:26.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java
@@ -1948,7 +1948,7 @@ else if (sraIDs.contains(rd.getSra_accession()))
                 }
 
                 File outDir = new File(getHelper().getWorkingDirectory(), "cachedReadData");
-                getTaskFileManagerImpl().addIntermediateFile(outDir);
+                getTaskFileManagerImpl().addDeferredIntermediateFile(outDir); // NOTE: this must be deferred so it remains until the end
 
                 File doneFile = new File(outDir, rd.getSra_accession() + ".done");
                 sraIDs.add(rd.getSra_accession());

Original file line number	Diff line number	Diff line change
`@@ -1948,7 +1948,7 @@ else if (sraIDs.contains(rd.getSra_accession()))`
`1948`	`1948`	`}`
`1949`	`1949`
`1950`	`1950`	`File outDir = new File(getHelper().getWorkingDirectory(), "cachedReadData");`
`1951`		`- getTaskFileManagerImpl().addIntermediateFile(outDir);`
	`1951`	`+ getTaskFileManagerImpl().addDeferredIntermediateFile(outDir); // NOTE: this must be deferred so it remains until the end`
`1952`	`1952`
`1953`	`1953`	`File doneFile = new File(outDir, rd.getSra_accession() + ".done");`
`1954`	`1954`	`sraIDs.add(rd.getSra_accession());`