Set workDir for DeepVariant/GLNexus

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java

@@ -283,7 +283,6 @@ public void execute(List<File> inputGvcfs, File outputVcf, PipelineOutputTracker
 
                 // Command will fail if this exists:
                 File dbDir = new File (outputVcf.getParentFile(), "GLnexus.DB");
-
                 if (dbDir.exists())
                 {
                     FileUtils.deleteDirectory(dbDir);
@@ -294,6 +293,7 @@ public void execute(List<File> inputGvcfs, File outputVcf, PipelineOutputTracker
                 throw new PipelineJobException(e);
             }
 
+            setWorkingDir(workDir);
             execute(Arrays.asList("/bin/bash", localBashScript.getPath()));
 
             if (!outputVcf.exists())

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java

@@ -284,6 +284,7 @@ public void execute(File inputBam, File refFasta, File outputGvcf, PipelineOutpu
                 throw new PipelineJobException(e);
             }
 
+            setWorkingDir(workDir);
             execute(Arrays.asList("/bin/bash", localBashScript.getPath()));
 
             if (!outputGvcf.exists())