Add debugging for nimble align

Author: bbimber

singlecell/src/org/labkey/singlecell/run/NimbleHelper.java

@@ -360,14 +360,13 @@ private Map<NimbleGenome, File> doAlignment(List<NimbleGenome> genomes, List<Fil
         alignArgs.add("--input");
         alignArgs.add("/work/" + localBam.getName());
 
-        File doneFile = getNimbleDoneFile(getPipelineCtx().getWorkingDirectory(), "align.all");
-
         boolean dockerRan = runUsingDocker(alignArgs, output, "align.all");
         for (NimbleGenome genome : genomes)
         {
             File alignResultsTsv = new File(getPipelineCtx().getWorkingDirectory(), "alignResults." + genome.genomeId + ".txt");
             if (dockerRan && !alignResultsTsv.exists())
             {
+                File doneFile = getNimbleDoneFile(getPipelineCtx().getWorkingDirectory(), "align.all");
                 if (doneFile.exists())
                 {
                     doneFile.delete();
@@ -540,6 +539,10 @@ private boolean runUsingDocker(List<String> nimbleArgs, PipelineStepOutput outpu
                 getPipelineCtx().getLogger().info("Nimble already completed, resuming: " + resumeString);
                 return false;
             }
+            else
+            {
+                getPipelineCtx().getLogger().debug("done file not found: " + doneFile.getPath());
+            }
         }
 
         SimpleScriptWrapper rWrapper = new SimpleScriptWrapper(getPipelineCtx().getLogger());