Add more pipeline logging

Author: bbimber

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

@@ -70,7 +70,7 @@ default void validateScatter(ScatterGatherMethod method, PipelineJob job) throws
 
         default void performAdditionalMergeTasks(SequenceOutputHandler.JobContext ctx, PipelineJob job, TaskFileManager manager, ReferenceGenome genome, List<File> orderedScatterOutputs, List<String> orderedJobDirs) throws PipelineJobException
         {
-
+            ctx.getLogger().debug("No additional merge tasks are implemented for: " + getClass().getName());
         }
 
         default boolean doSortAfterMerge()

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/SplitVcfBySamplesStep.java

@@ -96,6 +96,12 @@ public void performAdditionalMergeTasks(SequenceOutputHandler.JobContext ctx, Pi
         job.getLogger().info("Merging additional track VCFs");
         File inputVCF = ((SequenceJob)getPipelineCtx().getJob()).getInputFiles().get(0);
         List<File> firstJobOutputs = findProducedVcfs(inputVCF, new File(ctx.getWorkingDirectory(), orderedJobDirs.get(0)));
+        job.getLogger().info("total VCFs found in job dir: " + firstJobOutputs.size());
+        if (firstJobOutputs.isEmpty())
+        {
+            throw new PipelineJobException("No VCFs found in folder: " + new File(ctx.getWorkingDirectory(), orderedJobDirs.get(0)));
+        }
+
         for (File fn : firstJobOutputs)
         {
             List<File> toConcat = orderedJobDirs.stream().map(jobDir -> {