Dont double-create seurat object outputfile

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java

@@ -256,6 +256,9 @@ public Pair<File, File> downloadSra(String dataset, File outDir) throws Pipeline
 
             args.add(dataset);
 
+            //NOTE: sratoolkit requires this to be set:
+            addToEnvironment("HOME", System.getProperty("user.home"));
+
             execute(args);
 
             List<File> files = new ArrayList<>(Arrays.asList(Objects.requireNonNull(outDir.listFiles((dir, name) -> name.startsWith(dataset)))));

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

@@ -543,7 +543,15 @@ else if (step.createsSeuratObjects())
                     }
                 }
 
-                _resumer.getFileManager().addSequenceOutput(so);
+                //This indicates the job processed an input file, but did not create a new object (like running FindMarkers)
+                if (output.getSequenceOutputFileId() != null)
+                {
+                    ctx.getLogger().info("Sequence output already exists, will not re-create output for seurat object: " + output.getSequenceOutputFileId());
+                }
+                else
+                {
+                    _resumer.getFileManager().addSequenceOutput(so);
+                }
 
                 // This could be a little confusing, but add one record out seurat output, even though there is one HTML file::
                 SequenceOutputFile o = new SequenceOutputFile();