Bugfix to pipeline code for additional merge tasks

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java

@@ -877,9 +877,9 @@ public void performAdditionalMergeTasks(JobContext ctx, PipelineJob job, TaskFil
         List<PipelineStepCtx<VariantProcessingStep>> providers = SequencePipelineService.get().getSteps(job, VariantProcessingStep.class);
         for (PipelineStepCtx<VariantProcessingStep> stepCtx : providers)
         {
-            VariantProcessingStep step = stepCtx.getProvider().create(ctx);
-            if (step instanceof VariantProcessingStep.SupportsScatterGather)
+            if (stepCtx.getProvider() instanceof VariantProcessingStep.SupportsScatterGather)
             {
+                VariantProcessingStep step = stepCtx.getProvider().create(ctx);
                 ((VariantProcessingStep.SupportsScatterGather)step).performAdditionalMergeTasks(ctx, job, manager, genome, orderedScatterOutputs);
             }
         }

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceOutputHandlerJob.java

@@ -160,7 +160,7 @@ public File getSerializedOutputFilesFile()
     }
 
     @Override
-    public TaskPipeline getTaskPipeline()
+    public TaskPipeline<?> getTaskPipeline()
     {
         return  PipelineJobService.get().getTaskPipeline(new TaskId(SequenceOutputHandlerJob.class));
     }

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingRemoteMergeTask.java

@@ -237,6 +237,7 @@ private File runDefaultVariantMerge(JobContextImpl ctx, TaskFileManagerImpl mana
 
         if (handler instanceof VariantProcessingStep.SupportsScatterGather)
         {
+            ctx.getLogger().debug("Running additional merge tasks");
             ((VariantProcessingStep.SupportsScatterGather) handler).performAdditionalMergeTasks(ctx, getPipelineJob(), manager, genome, toConcat);
         }