Add more logging

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AlignerIndexUtil.java

@@ -98,8 +98,10 @@ private static boolean verifyOrCreateCachedIndex(PipelineContext ctx, @Nullable
 
                             destination = wd.inputFile(webserverIndexDir, destination, true);
                             if (output != null && !destination.equals(webserverIndexDir))
+                            {
+                                ctx.getLogger().debug("adding deferred delete file: " + destination.getPath());
                                 output.addDeferredDeleteIntermediateFile(destination);
-
+                            }
                             ctx.getLogger().info("finished copying files");
                         }
                         else

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

@@ -144,11 +144,6 @@ public void addStepOutputs(RecordedAction action, PipelineStepOutput output)
             addDeferredIntermediateFile(file);
         }
 
-        for (File file : output.getDeferredDeleteIntermediateFiles())
-        {
-            addDeferredIntermediateFile(file);
-        }
-
         for (PipelineStepOutput.SequenceOutput o : output.getSequenceOutputs())
         {
             addSequenceOutput(o.getFile(), o.getLabel(), o.getCategory(), o.getReadsetId(), o.getAnalysisId(), o.getGenomeId(), o.getDescription());