Updates to Save10xBarcodes

Author: bbimber

singlecell/src/org/labkey/singlecell/run/AbstractCellRangerDependentStep.java

@@ -88,6 +88,8 @@ protected File runCellRanger(AlignmentOutputImpl output, Readset rs, List<File>
             }
         }
 
+        NimbleHelper.write10xBarcodes(localBam, getWrapper().getLogger(), rs, referenceGenome, output);
+
         return localBam;
     }
 

singlecell/src/org/labkey/singlecell/run/NimbleAlignmentStep.java

@@ -109,10 +109,9 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
 
     private File createNimbleBam(AlignmentOutputImpl output, Readset rs, List<File> inputFastqs1, List<File> inputFastqs2) throws PipelineJobException
     {
-        File cellbarcodes = getCachedBarcodeFile(rs, true);
-        File umiMapping = getUmiMapping(cellbarcodes);
+        File cellBarcodeUmiMap = getCachedBarcodeFile(rs, true);
 
-        return NimbleHelper.runFastqToBam(output, getPipelineCtx(), rs, inputFastqs1, inputFastqs2, cellbarcodes, umiMapping);
+        return NimbleHelper.runFastqToBam(output, getPipelineCtx(), rs, inputFastqs1, inputFastqs2, cellBarcodeUmiMap);
     }
 
     private File getCachedBarcodeFile(Readset rs, boolean throwIfNotFound) throws PipelineJobException
@@ -132,18 +131,7 @@ private File getCachedBarcodeFile(Readset rs, boolean throwIfNotFound) throws Pi
         File ret = getPipelineCtx().getSequenceSupport().getCachedData(dataId);
         if (ret == null || ! ret.exists())
         {
-            throw new PipelineJobException("Missing cached cellbarcode file: " + dataId);
-        }
-
-        return ret;
-    }
-
-    private File getUmiMapping(File cellbarcodeFile) throws PipelineJobException
-    {
-        File ret = new File(cellbarcodeFile.getPath().replaceAll("cb.txt.gz", "umi.txt.gz"));
-        if (!ret.exists())
-        {
-            throw new PipelineJobException("Missing cached UMI file: " + ret.getPath());
+            throw new PipelineJobException("Missing cached cellbarcode/UMI file: " + dataId);
         }
 
         return ret;
@@ -156,7 +144,7 @@ private ExpData findCellBarcodeFiles(Readset rs) throws PipelineJobException
         TableInfo ti = us.getTable("outputfiles");
 
         SimpleFilter sf = new SimpleFilter(FieldKey.fromString("readset"), rs.getRowId());
-        sf.addCondition(FieldKey.fromString("category"), NimbleHelper.CATEGORY_CB);
+        sf.addCondition(FieldKey.fromString("category"), NimbleHelper.CATEGORY_CB_UMI);
         List<Integer> cbs = new TableSelector(ti, PageFlowUtil.set("dataid"), sf, new Sort("-rowid")).getArrayList(Integer.class);
         if (!cbs.isEmpty())
         {
@@ -194,8 +182,6 @@ private File performCellRangerAlignment(AlignmentOutputImpl output, Readset rs,
             }
         }
 
-        NimbleHelper.write10xBarcodes(localBam, getWrapper().getLogger(), rs, referenceGenome, output);
-
         return localBam;
     }
 

singlecell/src/org/labkey/singlecell/run/NimbleHelper.java

@@ -498,8 +498,7 @@ private Map<NimbleGenome, File> doAlignment(List<NimbleGenome> genomes, List<Fil
         return resultMap;
     }
 
-    public static final String CATEGORY_CB = "10x CellBarcode Map";
-    public static final String CATEGORY_UB = "10x UMI Map";
+    public static final String CATEGORY_CB_UMI = "10x CellBarcode/UMI Map";
 
     public static void write10xBarcodes(File bam, Logger log, Readset rs, ReferenceGenome referenceGenome, PipelineStepOutput output) throws PipelineJobException
     {
@@ -509,18 +508,13 @@ public static void write10xBarcodes(File bam, Logger log, Readset rs, ReferenceG
         barcodeArgs.add("-I");
         barcodeArgs.add(bam.getPath());
 
-        File cbOutput = new File(bam.getParentFile(), SequenceAnalysisService.get().getUnzippedBaseName(bam.getName()) + ".cb.txt.gz");
-        barcodeArgs.add("--cbOutput");
-        barcodeArgs.add(cbOutput.getPath());
-
-        File umiOutput = new File(bam.getParentFile(), SequenceAnalysisService.get().getUnzippedBaseName(bam.getName()) + ".umi.txt.gz");
-        barcodeArgs.add("--umiOutput");
-        barcodeArgs.add(umiOutput.getPath());
+        File bcOutput = new File(bam.getParentFile(), SequenceAnalysisService.get().getUnzippedBaseName(bam.getName()) + ".bc.txt.gz");
+        barcodeArgs.add("--output");
+        barcodeArgs.add(bcOutput.getPath());
 
         runner.execute(barcodeArgs);
 
-        output.addSequenceOutput(cbOutput, "10x CellBarcode Map: " + rs.getName(), CATEGORY_CB, rs.getReadsetId(), null, referenceGenome.getGenomeId(), null);
-        output.addSequenceOutput(umiOutput, "10x UMI Map: " + rs.getName(), CATEGORY_UB, rs.getReadsetId(), null, referenceGenome.getGenomeId(), null);
+        output.addSequenceOutput(bcOutput, "10x CellBarcode/UMI Map: " + rs.getName(), CATEGORY_CB_UMI, rs.getReadsetId(), null, referenceGenome.getGenomeId(), null);
     }
 
     public static File runNimbleReport(File alignResultsGz, int genomeId, PipelineStepOutput output, PipelineContext ctx) throws PipelineJobException
@@ -600,7 +594,7 @@ private static File getNimbleDoneFile(File parentDir, String resumeString)
         return new File(parentDir, "nimble." + resumeString + ".done");
     }
 
-    public static File runFastqToBam(PipelineStepOutput output, PipelineContext ctx, Readset rs, List<File> inputFastqs1, List<File> inputFastqs2, File cellBarcodes, File umiMapping) throws PipelineJobException
+    public static File runFastqToBam(PipelineStepOutput output, PipelineContext ctx, Readset rs, List<File> inputFastqs1, List<File> inputFastqs2, File cellBarcodeUmiMap) throws PipelineJobException
     {
         List<File> outputBams = new ArrayList<>();
         int bamIdx = 0;
@@ -632,11 +626,8 @@ public static File runFastqToBam(PipelineStepOutput output, PipelineContext ctx,
             args.add("--r2-fastq");
             args.add(inputFastqs2.get(bamIdx).getPath());
 
-            args.add("--cell-barcodes");
-            args.add(cellBarcodes.getPath());
-
-            args.add("--umi-mapping");
-            args.add(umiMapping.getPath());
+            args.add("--map");
+            args.add(cellBarcodeUmiMap.getPath());
 
             args.add("--output");
             args.add(outputBam.getPath());