Ensure SRA data not deleted until end of job

bbimber · bbimber · commit e285a64a289d · 2024-08-07T06:00:12.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java
@@ -1888,7 +1888,7 @@ private void restoreArchivedReadDataIfNeeded(Readset rs) throws PipelineJobExcep
                 }
 
                 File outDir = new File(getHelper().getWorkingDirectory(), "cachedReadData");
-                getTaskFileManagerImpl().addIntermediateFile(outDir);
+                getTaskFileManagerImpl().addDeferredIntermediateFile(outDir);
 
                 File doneFile = new File(outDir, rd.getSra_accession() + ".done");
                 RestoreSraDataHandler.FastqDumpWrapper sra = new RestoreSraDataHandler.FastqDumpWrapper(getJob().getLogger());

Original file line number	Diff line number	Diff line change
`@@ -1888,7 +1888,7 @@ private void restoreArchivedReadDataIfNeeded(Readset rs) throws PipelineJobExcep`
`1888`	`1888`	`}`
`1889`	`1889`
`1890`	`1890`	`File outDir = new File(getHelper().getWorkingDirectory(), "cachedReadData");`
`1891`		`- getTaskFileManagerImpl().addIntermediateFile(outDir);`
	`1891`	`+ getTaskFileManagerImpl().addDeferredIntermediateFile(outDir);`
`1892`	`1892`
`1893`	`1893`	`File doneFile = new File(outDir, rd.getSra_accession() + ".done");`
`1894`	`1894`	`RestoreSraDataHandler.FastqDumpWrapper sra = new RestoreSraDataHandler.FastqDumpWrapper(getJob().getLogger());`