Bugfix to NimbleAlignmentStep

Author: bbimber

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

@@ -141,7 +141,7 @@ private File getCachedBarcodeFile(Readset rs, boolean throwIfNotFound) throws Pi
     private File getUmiMapping(File cellbarcodeFile) throws PipelineJobException
     {
         File ret = new File(cellbarcodeFile.getPath().replaceAll("cb.txt.gz", "umi.txt.gz"));
-        if (ret == null || ! ret.exists())
+        if (!ret.exists())
         {
             throw new PipelineJobException("Missing cached UMI file: " + ret.getPath());
         }

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

@@ -8,6 +8,7 @@
 import org.labkey.api.sequenceanalysis.pipeline.AlignmentOutputImpl;
 import org.labkey.api.sequenceanalysis.pipeline.AlignmentStep;
 import org.labkey.api.sequenceanalysis.pipeline.AlignmentStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.IndexOutputImpl;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
 import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
 import org.labkey.api.sequenceanalysis.pipeline.SamtoolsRunner;
@@ -53,7 +54,7 @@ public NimbleBulkAlignmentStep(AlignmentStepProvider<?> provider, PipelineContex
     @Override
     public IndexOutput createIndex(ReferenceGenome referenceGenome, File outputDir) throws PipelineJobException
     {
-        return null;
+        return new IndexOutputImpl(referenceGenome);
     }
 
     @Override