Fix order in which seurat outputs are tagged

Author: bbimber

singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java

@@ -478,21 +478,24 @@ else if (step.createsSeuratObjects())
 
                 _resumer.getFileManager().addStepOutputs(action, output);
 
-                if (output.getSeuratObjects() != null && !output.getSeuratObjects().isEmpty())
+                if (step.createsSeuratObjects())
                 {
-                    currentFiles = new ArrayList<>(output.getSeuratObjects());
-                    Set<File> possibleIntermediates = currentFiles.stream().map(SingleCellStep.SeuratObjectWrapper::getFile).collect(Collectors.toSet());
-                    possibleIntermediates.removeAll(originalInputs);
-                    if (!possibleIntermediates.isEmpty())
+                    if (output.getSeuratObjects() != null && !output.getSeuratObjects().isEmpty())
                     {
-                        _resumer.getFileManager().addIntermediateFiles(possibleIntermediates);
-                        _resumer.getFileManager().addIntermediateFiles(possibleIntermediates.stream().map(x -> CellHashingServiceImpl.get().getCellBarcodesFromSeurat(x)).collect(Collectors.toSet()));
-                        _resumer.getFileManager().addIntermediateFiles(possibleIntermediates.stream().map(x -> CellHashingServiceImpl.get().getMetaTableFromSeurat(x)).collect(Collectors.toSet()));
+                        currentFiles = new ArrayList<>(output.getSeuratObjects());
+                        Set<File> possibleIntermediates = currentFiles.stream().map(SingleCellStep.SeuratObjectWrapper::getFile).collect(Collectors.toSet());
+                        possibleIntermediates.removeAll(originalInputs);
+                        if (!possibleIntermediates.isEmpty())
+                        {
+                            _resumer.getFileManager().addIntermediateFiles(possibleIntermediates);
+                            _resumer.getFileManager().addIntermediateFiles(possibleIntermediates.stream().map(x -> CellHashingServiceImpl.get().getCellBarcodesFromSeurat(x)).collect(Collectors.toSet()));
+                            _resumer.getFileManager().addIntermediateFiles(possibleIntermediates.stream().map(x -> CellHashingServiceImpl.get().getMetaTableFromSeurat(x)).collect(Collectors.toSet()));
+                        }
+                    }
+                    else
+                    {
+                        throw new PipelineJobException("Expected step to create seurat objects but none reported");
                     }
-                }
-                else if (step.createsSeuratObjects())
-                {
-                    throw new PipelineJobException("Expected step to create seurat objects but none reported");
                 }
                 else
                 {