Allow cellranger to avoid FASTQ merge

Author: bbimber

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

@@ -280,6 +280,12 @@ public IndexOutput createIndex(ReferenceGenome referenceGenome, File outputDir)
         return output;
     }
 
+    @Override
+    public boolean canAlignMultiplePairsAtOnce()
+    {
+        return true;
+    }
+
     @Override
     public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nullable List<File> inputFastqs2, File outputDirectory, ReferenceGenome referenceGenome, String basename, String readGroupId, @Nullable String platformUnit) throws PipelineJobException
     {

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

@@ -256,12 +256,17 @@ public AlignmentStep.IndexOutput createIndex(ReferenceGenome referenceGenome, Fi
 
                 //recache if not already
                 AlignerIndexUtil.saveCachedIndex(hasCachedIndex, getPipelineCtx(), indexDir, getIndexCachedDirName(getPipelineCtx().getJob()), referenceGenome);
-
             }
 
             return output;
         }
 
+        @Override
+        public boolean canAlignMultiplePairsAtOnce()
+        {
+            return true;
+        }
+
         @Override
         public AlignmentStep.AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nullable List<File> inputFastqs2, File outputDirectory, ReferenceGenome referenceGenome, String basename, String readGroupId, @Nullable String platformUnit) throws PipelineJobException
         {