Skip cellranger-specific complete steps

Author: bbimber

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

@@ -6,14 +6,18 @@
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
+import org.labkey.api.sequenceanalysis.SequenceOutputFile;
+import org.labkey.api.sequenceanalysis.model.AnalysisModel;
 import org.labkey.api.sequenceanalysis.model.Readset;
 import org.labkey.api.sequenceanalysis.pipeline.AlignmentOutputImpl;
 import org.labkey.api.sequenceanalysis.pipeline.AlignmentStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
 import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
+import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport;
 
 import java.io.File;
 import java.io.IOException;
+import java.util.Collection;
 import java.util.List;
 
 public class AbstractCellRangerDependentStep extends CellRangerGexCountStep
@@ -87,6 +91,12 @@ protected File runCellRanger(AlignmentOutputImpl output, Readset rs, List<File>
         return localBam;
     }
 
+    @Override
+    public void complete(SequenceAnalysisJobSupport support, AnalysisModel model, Collection<SequenceOutputFile> outputFilesCreated) throws PipelineJobException
+    {
+        // Skip GEX-specific complete steps.
+    }
+
     @Override
     public boolean alwaysCopyIndexToWorkingDir()
     {

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

@@ -28,7 +28,7 @@ public class NimbleAlignmentStep extends AbstractCellRangerDependentStep
     public static final String ALIGN_OUTPUT = "alignmentOutput";
     public static final String STRANDEDNESS = "strandedness";
 
-    public NimbleAlignmentStep(AlignmentStepProvider provider, PipelineContext ctx, CellRangerWrapper wrapper)
+    public NimbleAlignmentStep(AlignmentStepProvider<?> provider, PipelineContext ctx, CellRangerWrapper wrapper)
     {
         super(provider, ctx, wrapper);
     }