Another fix for jobs with archived readsets

Author: bbimber

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

@@ -34,7 +34,7 @@ protected SequenceReadsetHandlerJob()
     {
     }
 
-    public SequenceReadsetHandlerJob(Container c, User user, @Nullable String jobName, PipeRoot pipeRoot, SequenceOutputHandler handler, List<SequenceReadsetImpl> readsets, JSONObject jsonParams) throws IOException
+    public SequenceReadsetHandlerJob(Container c, User user, @Nullable String jobName, PipeRoot pipeRoot, SequenceOutputHandler<?> handler, List<SequenceReadsetImpl> readsets, JSONObject jsonParams) throws IOException
     {
         super(SequenceReadsetHandlerPipelineProvider.NAME, c, user, jobName, pipeRoot, jsonParams, null, SequenceOutputHandlerJob.FOLDER_NAME);
 
@@ -50,7 +50,7 @@ public SequenceReadsetHandlerJob(Container c, User user, @Nullable String jobNam
     }
 
     @Override
-    public TaskPipeline getTaskPipeline()
+    public TaskPipeline<?> getTaskPipeline()
     {
         return  PipelineJobService.get().getTaskPipeline(new TaskId(SequenceReadsetHandlerJob.class));
     }
@@ -81,7 +81,11 @@ public List<File> getInputFiles()
             {
                 for (ReadData d : rs.getReadData())
                 {
-                    ret.add(d.getFile1());
+                    if (d.getFile1() != null)
+                    {
+                        ret.add(d.getFile1());
+                    }
+
                     if (d.getFile2() != null)
                     {
                         ret.add(d.getFile2());