Bugfix to BAM-less jobs

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAnalysisTask.java

@@ -365,7 +365,7 @@ private void processAnalyses(AnalysisModelImpl analysisModel, int runId, List<Re
             getJob().getLogger().info("no analyses were selected");
         }
 
-        File bam = ExperimentService.get().getExpData(analysisModel.getAlignmentFile()).getFile();
+        File bam = analysisModel.getAlignmentFile() == null ? null : ExperimentService.get().getExpData(analysisModel.getAlignmentFile()).getFile();
         if (bam == null)
         {
             getJob().getLogger().error("unable to find BAM, skipping");

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

@@ -18,7 +18,7 @@
 
 public class AbstractCellRangerDependentStep extends CellRangerGexCountStep
 {
-    public AbstractCellRangerDependentStep(AlignmentStepProvider provider, PipelineContext ctx, CellRangerWrapper wrapper)
+    public AbstractCellRangerDependentStep(AlignmentStepProvider<?> provider, PipelineContext ctx, CellRangerWrapper wrapper)
     {
         super(provider, ctx, wrapper);
     }