Allow single-cell pipeline to use raw counts or seurat object as input

Author: bbimber

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

@@ -124,9 +124,6 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra
             output.setSeuratObjects(outputs);
         }
 
-        output.setHtmlFile(getExpectedHtmlFile(ctx, outputPrefix));
-        output.setMarkdownFile(getExpectedMarkdownFile(ctx, outputPrefix));
-
         return output;
     }
 

singlecell/src/org/labkey/singlecell/SingleCellModule.java

@@ -30,11 +30,13 @@
 import org.labkey.api.singlecell.pipeline.SingleCellStep;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.view.WebPartFactory;
+import org.labkey.singlecell.analysis.AbstractSingleCellHandler;
 import org.labkey.singlecell.analysis.CellHashingHandler;
 import org.labkey.singlecell.analysis.CellRangerRawDataHandler;
 import org.labkey.singlecell.analysis.CellRangerSeuratHandler;
 import org.labkey.singlecell.analysis.CiteSeqHandler;
 import org.labkey.singlecell.analysis.LoupeCellHashingHandler;
+import org.labkey.singlecell.analysis.ProcessSeuratObjectHandler;
 import org.labkey.singlecell.analysis.ProcessSingleCellHandler;
 import org.labkey.singlecell.analysis.SeuratCellHashingHandler;
 import org.labkey.singlecell.analysis.SeuratCiteSeqHandler;
@@ -155,6 +157,7 @@ public static void registerPipelineSteps()
         SequenceAnalysisService.get().registerFileHandler(new CellRangerSeuratHandler());
         SequenceAnalysisService.get().registerFileHandler(new CellRangerRawDataHandler());
         SequenceAnalysisService.get().registerFileHandler(new ProcessSingleCellHandler());
+        SequenceAnalysisService.get().registerFileHandler(new ProcessSeuratObjectHandler());
 
         //Single-cell:
         SequencePipelineService.get().registerPipelineStep(new AppendCiteSeq.Provider());
@@ -185,7 +188,7 @@ public static void registerPipelineSteps()
     public Set<Class> getUnitTests()
     {
         return PageFlowUtil.set(
-                ProcessSingleCellHandler.TestCase.class
+                AbstractSingleCellHandler.TestCase.class
         );
     }
 }