Bugfix to split VCF jobs

Author: bbimber

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

@@ -95,17 +95,17 @@ 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)));
+        List<File> firstJobOutputs = findProducedVcfs(inputVCF, new File(ctx.getSourceDirectory(), 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)));
+            throw new PipelineJobException("No VCFs found in folder: " + new File(ctx.getSourceDirectory(), orderedJobDirs.get(0)));
         }
 
         for (File fn : firstJobOutputs)
         {
             List<File> toConcat = orderedJobDirs.stream().map(jobDir -> {
-                File f = new File(new File(getPipelineCtx().getWorkingDirectory(), jobDir), fn.getName());
+                File f = new File(new File(getPipelineCtx().getSourceDirectory(), jobDir), fn.getName());
                 if (!f.exists())
                 {
                     throw new IllegalStateException("Missing file: " + f.getPath());