Support native-pair-hmm-threads for HaplotypeCaller

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/HaplotypeCallerWrapper.java

@@ -4,6 +4,7 @@
 import org.apache.logging.log4j.Logger;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.pipeline.SamtoolsIndexer;
+import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.sequenceanalysis.run.AbstractGatk4Wrapper;
 import org.labkey.sequenceanalysis.pipeline.ReblockGvcfHandler;
 import org.labkey.sequenceanalysis.util.SequenceUtil;
@@ -58,6 +59,13 @@ public void execute(File inputBamOrCram, File referenceFasta, File outputFile, L
             args.addAll(options);
         }
 
+        Integer maxThreads = SequencePipelineService.get().getMaxThreads(getLogger());
+        if (maxThreads != null)
+        {
+            args.add("--native-pair-hmm-threads");
+            args.add(maxThreads.toString());
+        }
+
         args.add("-ERC");
         args.add("GVCF");