Bugfix GenomicsDBImport

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/bampostprocessing/MarkDuplicatesWithMateCigarStep.java

@@ -36,7 +36,7 @@ public Provider()
         {
             super("MarkDuplicatesWithMateCigarStep", "Mark Duplicates With Mate", "Picard", "This runs Picard tools MarkDuplicatesWithMateCigarStep command in order to mark and/or remove duplicate reads.  Unlike the original MarkDuplicates, this uses paired read information to more accurately detect true duplicates.  Please note this can have implications for downstream analysis, because reads marked as duplicates are frequently omitted.  This is often desired, but can be a problem for sequencing of PCR products.", Arrays.asList(
                     ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("REMOVE_DUPLICATES"), "removeDuplicates", "Remove Duplicates", "If selected, duplicate reads will be removed, as opposed to flagged as duplicates.", "checkbox", null, null),
-                    ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("MINIMUM_DISTANCE"), "minimumDistance", "Minimum Distance", "The minimum distance to buffer records to account for clipping on the 5' end of the records.", "ldk-integerfield", null, null)
+                    ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("MINIMUM_DISTANCE"), "minimumDistance", "Minimum Distance", "The minimum distance to buffer records to account for clipping on the 5' end of the records.", "ldk-integerfield", null, 150)
             ), null, "http://picard.sourceforge.net/command-line-overview.shtml");
         }
 

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

@@ -454,7 +454,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
 
             Set<File> toDelete = new HashSet<>();
             File doneFile = new File(destinationWorkspaceFolder, "genomicsdb.done");
-            File startedFile = new File(destinationWorkspaceFolder, "genomicsdb.started");
+            File startedFile = new File(destinationWorkspaceFolder.getParentFile(), "genomicsdb.started");
             boolean genomicsDbCompleted = doneFile.exists();
             boolean genomicsDbStarted = startedFile.exists();
             ctx.getFileManager().addIntermediateFile(doneFile);