Bugfix to mGAP track generator (#131)

* Bugfix to mGAP track task

Author: bbimber

mGAP/src/org/labkey/mgap/pipeline/GenerateMgapTracksStep.java

@@ -469,8 +469,8 @@ public void performAdditionalMergeTasks(SequenceOutputHandler.JobContext ctx, Pi
         }
 
         job.getLogger().info("Merging novel sites VCF");
-        List<File> toConcat = orderedScatterOutputs.stream().map(f -> {
-            f = getNovelSitesOutput(f.getParentFile());
+        List<File> toConcat = orderedJobDirs.stream().map(dirName -> {
+            File f = getNovelSitesOutput(new File(ctx.getSourceDirectory(), dirName));
             if (!f.exists())
             {
                 throw new IllegalStateException("Missing file: " + f.getPath());
@@ -482,6 +482,11 @@ public void performAdditionalMergeTasks(SequenceOutputHandler.JobContext ctx, Pi
             return f;
         }).toList();
 
+        if (toConcat.isEmpty())
+        {
+            throw new PipelineJobException("No novel sites VCFs found");
+        }
+
         String basename = SequenceAnalysisService.get().getUnzippedBaseName(toConcat.get(0).getName());
         File combined = new File(ctx.getSourceDirectory(), basename + ".vcf.gz");
         File combinedIdx = new File(combined.getPath() + ".tbi");