Cache bwamem2 indexes by default

Author: bbimber

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

@@ -63,7 +63,7 @@ public List<String> getProtocolActionNames()
         }
 
         @Override
-        public PipelineJob.Task createTask(PipelineJob job)
+        public PipelineJob.Task<?> createTask(PipelineJob job)
         {
             return new CacheAlignerIndexesTask(this, job);
         }

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWAMem2Wrapper.java

@@ -74,6 +74,8 @@ public Provider()
 
                     }}, null)
             ), null, "https://github.com/bwa-mem2/bwa-mem2", true, true);
+
+            setAlwaysCacheIndex(true);
         }
 
         @Override