Always include placeholder for SAMPLE_NAME in FastqToSam

Author: bbimber

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

@@ -255,7 +255,7 @@ public IndexOutput createIndex(ReferenceGenome referenceGenome, File outputDir)
                 }
 
                 List<String> args = new ArrayList<>();
-                args.add(getWrapper().getExe().getPath());
+                args.add(getWrapper().getExe(true).getPath());
                 args.add("mkref");
                 args.add("--fasta=" + referenceGenome.getWorkingFastaFile().getPath());
                 args.add("--genes=" + gtfFile.getPath());
@@ -296,7 +296,7 @@ public AlignmentOutput performAlignment(Readset rs, File inputFastq1, @Nullable
             AlignmentOutputImpl output = new AlignmentOutputImpl();
 
             List<String> args = new ArrayList<>();
-            args.add(getWrapper().getExe().getPath());
+            args.add(getWrapper().getExe(false).getPath());
             args.add("count");
 
             //TODO: consider always adding this?
@@ -671,7 +671,7 @@ public void complete(SequenceAnalysisJobSupport support, AnalysisModel model) th
     public File runAggr(String id, File csvFile, List<String> extraArgs) throws PipelineJobException
     {
         List<String> args = new ArrayList<>();
-        args.add(getExe().getPath());
+        args.add(getExe(false).getPath());
         args.add("aggr");
 
         id = id.replaceAll("[^a-zA-z0-9_\\-]", "_");
@@ -698,7 +698,7 @@ public File runAggr(String id, File csvFile, List<String> extraArgs) throws Pipe
     public File runReanalyze(File matrix, File outDir, String id, List<String> extraParams) throws PipelineJobException
     {
         List<String> args = new ArrayList<>();
-        args.add(getExe().getPath());
+        args.add(getExe(false).getPath());
         args.add("reanalyze");
 
         id = id.replaceAll("[^a-zA-z0-9_\\-]", "_");
@@ -723,9 +723,9 @@ public File runReanalyze(File matrix, File outDir, String id, List<String> extra
         return output;
     }
 
-    protected File getExe()
+    protected File getExe(boolean use31)
     {
-        return SequencePipelineService.get().getExeForPackage("CELLRANGERPATH", "cellranger");
+        return SequencePipelineService.get().getExeForPackage("CELLRANGERPATH", "cellranger" + (use31 ? "-31" : ""));
     }
 
     public static Set<File> getRawDataDirs(File outputDir, boolean filteredOnly)

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

@@ -75,8 +75,7 @@ private List<String> getParams(File file, File file2, SAMFileHeader.SortOrder so
             if (rg.getPlatformUnit() != null)
                 params.add("PLATFORM_UNIT=" + rg.getPlatformUnit());
 
-            if (rg.getPlatformUnit() != null)
-                params.add("SAMPLE_NAME=" + rg.getSample());
+            params.add("SAMPLE_NAME=" + (rg.getSample() == null ? "SAMPLE" : rg.getSample()));
         }
         else
         {