Bugfix to nimble aligner step

Author: bbimber

singlecell/src/org/labkey/singlecell/SingleCellController.java

@@ -325,6 +325,10 @@ private static void validateBarcodes(List<Map<String, Object>> readsetRows, Cont
             if (rs.get("barcode5") != null) {
                 uniqueBarcodeNames.add((String.valueOf(rs.get("barcode5"))));
             }
+
+            if (rs.get("barcode3") != null) {
+                uniqueBarcodeNames.add((String.valueOf(rs.get("barcode3"))));
+            }
         });
 
         if (!uniqueBarcodeNames.isEmpty())

singlecell/src/org/labkey/singlecell/run/NimbleAligner.java

@@ -79,20 +79,20 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
     {
         File localBam = new File(outputDirectory, basename + ".cellranger.bam");
         File localBamIdx = new File(localBam.getPath() + ".bai");
-        AlignmentOutput output;
+        AlignmentOutputImpl output = new AlignmentOutputImpl();;
 
         if (localBam.exists() && localBamIdx.exists())
         {
             getPipelineCtx().getLogger().info("Existing BAM found, re-using: " + localBam.getPath());
-            output = new AlignmentOutputImpl();
         }
         else
         {
             getPipelineCtx().getLogger().info("Running cellranger");
-            output = super.performAlignment(rs, inputFastqs1, inputFastqs2, outputDirectory, referenceGenome, basename, readGroupId, platformUnit);
+            AlignmentOutput crOutput = super.performAlignment(rs, inputFastqs1, inputFastqs2, outputDirectory, referenceGenome, basename, readGroupId, platformUnit);
 
             // Remove all the normal 10x outputs:
-            output.getSequenceOutputs().clear();
+            output.addCommandsExecuted(crOutput.getCommandsExecuted());
+            output.addIntermediateFiles(crOutput.getIntermediateFiles());
 
             // Remove the whole 10x folder:
             output.addIntermediateFile(output.getBAM().getParentFile().getParentFile());