Add complete() method for VariantProcessingStep and create step to auto-create/update release tracks for mGAP

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/VariantProcessingStep.java

@@ -38,6 +38,11 @@ default void init(PipelineJob job, SequenceAnalysisJobSupport support, List<Sequ
 
     }
 
+    default void complete(PipelineJob job, List<SequenceOutputFile> inputs, List<SequenceOutputFile> outputsCreated, SequenceAnalysisJobSupport support) throws PipelineJobException
+    {
+
+    }
+
     enum ScatterGatherMethod
     {
         none(),

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

@@ -696,13 +696,25 @@ public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport
         {
 
         }
+
+        @Override
+        public void complete(PipelineJob job, List<SequenceOutputFile> inputs, List<SequenceOutputFile> outputsCreated, SequenceAnalysisJobSupport support) throws PipelineJobException
+        {
+            SequenceTaskHelper taskHelper = new SequenceTaskHelper(getPipelineJob(job), getPipelineJob(job).getDataDirectory());
+            List<PipelineStepCtx<VariantProcessingStep>> providers = SequencePipelineService.get().getSteps(job, VariantProcessingStep.class);
+            for (PipelineStepCtx<VariantProcessingStep> stepCtx : providers)
+            {
+                VariantProcessingStep step = stepCtx.getProvider().create(taskHelper);
+                step.complete(job, inputs, outputsCreated, support);
+            }
+        }
     }
 
     @Override
     public Collection<String> getAllowableActionNames()
     {
         Set<String> allowableNames = new HashSet<>();
-        for (PipelineStepProvider provider: SequencePipelineService.get().getProviders(VariantProcessingStep.class))
+        for (PipelineStepProvider<?> provider: SequencePipelineService.get().getProviders(VariantProcessingStep.class))
         {
             allowableNames.add(provider.getLabel());
         }