Separate requirement for hashing and cite-seq data

Author: bbimber

singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java

@@ -169,7 +169,13 @@ protected List<Chunk> getChunks() throws PipelineJobException
     }
 
     @Override
-    public boolean requiresHashingOrCiteSeq()
+    public boolean requiresHashing()
+    {
+        return false;
+    }
+
+    @Override
+    public boolean requiresCiteSeq()
     {
         return false;
     }

singlecell/api-src/org/labkey/api/singlecell/pipeline/SingleCellStep.java

@@ -32,7 +32,9 @@ default boolean createsSeuratObjects()
         return true;
     }
 
-    public boolean requiresHashingOrCiteSeq();
+    public boolean requiresCiteSeq();
+
+    public boolean requiresHashing();
 
     public boolean isIncluded(SequenceOutputHandler.JobContext ctx, List<SequenceOutputFile> inputs) throws PipelineJobException;
 

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

@@ -136,16 +136,22 @@ public Processor(boolean doProcessRawCounts)
         @Override
         public void init(JobContext ctx, List<SequenceOutputFile> inputFiles, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException
         {
-            boolean requiresHashingOrCite = false;
+            boolean requiresHashing = false;
+            boolean requiresCite = false;
             List<PipelineStepCtx<SingleCellStep>> steps = SequencePipelineService.get().getSteps(ctx.getJob(), SingleCellStep.class);
             for (PipelineStepCtx<SingleCellStep> stepCtx : steps)
             {
                 SingleCellStep step = stepCtx.getProvider().create(ctx);
                 step.init(ctx, inputFiles);
 
-                if (step.requiresHashingOrCiteSeq())
+                if (step.requiresCiteSeq())
                 {
-                    requiresHashingOrCite = true;
+                    requiresCite = true;
+                }
+
+                if (step.requiresHashing())
+                {
+                    requiresHashing = true;
                 }
 
                 for (ToolParameterDescriptor pd : stepCtx.getProvider().getParameters())
@@ -159,9 +165,9 @@ public void init(JobContext ctx, List<SequenceOutputFile> inputFiles, List<Recor
                 }
             }
 
-            if (requiresHashingOrCite)
+            if (requiresCite || requiresHashing)
             {
-                CellHashingService.get().prepareHashingAndCiteSeqFilesIfNeeded(ctx.getSourceDirectory(), ctx.getJob(), ctx.getSequenceSupport(), "readsetId", false, false);
+                CellHashingServiceImpl.get().prepareHashingAndCiteSeqFilesIfNeeded(ctx.getSourceDirectory(), ctx.getJob(), ctx.getSequenceSupport(), "readsetId", false, false, true, requiresHashing, requiresCite);
             }
         }
 

singlecell/src/org/labkey/singlecell/pipeline/singlecell/AbstractCellHashingCiteseqStep.java

@@ -83,11 +83,5 @@ protected String getRelativePath(File target, File outputDir)
         return FileUtil.relativePath(outputDir.getPath(), target.getPath());
     }
 
-    @Override
-    public boolean requiresHashingOrCiteSeq()
-    {
-        return true;
-    }
-
     abstract protected Map<Integer, File> prepareCountData(SingleCellOutput output, SequenceOutputHandler.JobContext ctx, List<SeuratObjectWrapper> inputObjects, String outputPrefix) throws PipelineJobException;
 }

singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendCiteSeq.java

@@ -57,6 +57,12 @@ private static List<ToolParameterDescriptor> getParams()
         return ret;
     }
 
+    @Override
+    public boolean requiresCiteSeq()
+    {
+        return true;
+    }
+
     @Override
     public String getFileSuffix()
     {

singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunCellHashing.java

@@ -42,6 +42,12 @@ public RunCellHashing create(PipelineContext ctx)
         }
     }
 
+    @Override
+    public boolean requiresHashing()
+    {
+        return true;
+    }
+
     @Override
     public Collection<String> getRLibraries()
     {