Bugfix to scatter/gather

bbimber · bbimber · commit 6681142c4880 · 2023-09-29T06:09:49.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java
@@ -879,7 +879,8 @@ public void performAdditionalMergeTasks(JobContext ctx, PipelineJob job, TaskFil
         List<PipelineStepCtx<VariantProcessingStep>> providers = SequencePipelineService.get().getSteps(job, VariantProcessingStep.class);
         for (PipelineStepCtx<VariantProcessingStep> stepCtx : providers)
         {
-            if (stepCtx.getProvider() instanceof VariantProcessingStep.SupportsScatterGather ssg)
+            VariantProcessingStep vps = stepCtx.getProvider().create(ctx);
+            if (vps instanceof VariantProcessingStep.SupportsScatterGather ssg)
             {
                 ssg.performAdditionalMergeTasks(ctx, job, manager, genome, orderedScatterOutputs, orderedJobDirs);
             }

Original file line number	Diff line number	Diff line change
`@@ -879,7 +879,8 @@ public void performAdditionalMergeTasks(JobContext ctx, PipelineJob job, TaskFil`
`879`	`879`	`List<PipelineStepCtx<VariantProcessingStep>> providers = SequencePipelineService.get().getSteps(job, VariantProcessingStep.class);`
`880`	`880`	`for (PipelineStepCtx<VariantProcessingStep> stepCtx : providers)`
`881`	`881`	`{`
`882`		`- if (stepCtx.getProvider() instanceof VariantProcessingStep.SupportsScatterGather ssg)`
	`882`	`+ VariantProcessingStep vps = stepCtx.getProvider().create(ctx);`
	`883`	`+ if (vps instanceof VariantProcessingStep.SupportsScatterGather ssg)`
`883`	`884`	`{`
`884`	`885`	`ssg.performAdditionalMergeTasks(ctx, job, manager, genome, orderedScatterOutputs, orderedJobDirs);`
`885`	`886`	`}`