Dont delete count matrix folder for CITE-seq

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/CellHashingHandler.java

@@ -299,8 +299,11 @@ public void processFilesRemote(List<Readset> readsets, JobContext ctx) throws Un
                     {
                         ctx.getLogger().debug("HTO calls will not be generated");
 
-                        File citeSeqCount = (File) callMap.get("citeSeqCount");
+                        File citeSeqCount = (File) callMap.get("citeSeqCountMatrix");
                         ctx.getFileManager().addSequenceOutput(citeSeqCount, rs.getName() + ": CITE-Seq Count Matrix","CITE-Seq Count Matrix", rs.getReadsetId(), null, null, null);
+
+                        File outDir = (File) callMap.get("outDir");
+                        ctx.getFileManager().removeIntermediateFile(outDir);
                     }
 
                     File origUnknown = getCiteSeqCountUnknownOutput(ctx.getSourceDirectory(), bestEditDistance);
@@ -390,7 +393,8 @@ private Map<String, Object> executeCiteSeqCount(JobContext ctx, RecordedAction a
         ctx.getFileManager().addIntermediateFile(outputDir);
 
         Map<String, Object> callMap = new HashMap<>();
-        callMap.put("citeSeqCount", outputMatrix);
+        callMap.put("citeSeqCountMatrix", outputMatrix);
+        callMap.put("outputDir", outputDir);
 
         if (generateHtoCalls)
         {

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/TaskFileManagerImpl.java

@@ -692,6 +692,12 @@ public void deleteIntermediateFiles() throws PipelineJobException
 
                 if (f.getParentFile().listFiles().length == 0)
                 {
+                    //Do not delete the primary working directory
+                    if (_wd != null && _wd.getDir().equals(f.getParentFile()))
+                    {
+                        continue;
+                    }
+
                     _job.getLogger().debug("\talso deleting empty parent folder: " + f.getParentFile().getPath());
                     f.getParentFile().delete();
                 }