Bugfix to Save10xBarcodes

Author: bbimber

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

@@ -328,7 +328,7 @@ private boolean shouldDiscardBam()
             return false;
         }
 
-        return !_alwaysRetainBam &&  getProvider().getParameterByName(AbstractAlignmentStepProvider.DISCARD_BAM).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false);
+        return !_alwaysRetainBam && getProvider().getParameterByName(AbstractAlignmentStepProvider.DISCARD_BAM).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false);
     }
 
     private boolean _alwaysRetainBam = false;
@@ -349,7 +349,7 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
         AbstractAlignmentStepProvider.ALIGNMENT_MODE mode = AbstractAlignmentStepProvider.ALIGNMENT_MODE.valueOf(alignmentMode);
 
         List<Pair<File, File>> inputFastqs = new ArrayList<>();
-        for (int i = 0; i < inputFastqs1.size();i++)
+        for (int i = 0; i < inputFastqs1.size(); i++)
         {
             File inputFastq1 = inputFastqs1.get(i);
             File inputFastq2 = inputFastqs2.get(i);
@@ -395,9 +395,14 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
         File outdir = new File(outputDirectory, id);
         outdir = new File(outdir, "outs");
 
+        File bam = new File(outdir, "possorted_genome_bam.bam");
+        if (bam.exists())
+        {
+            NimbleHelper.write10xBarcodes(bam, getWrapper().getLogger(), rs, referenceGenome, output);
+        }
+
         if (!shouldDiscardBam())
         {
-            File bam = new File(outdir, "possorted_genome_bam.bam");
             if (!bam.exists())
             {
                 throw new PipelineJobException("Unable to find file: " + bam.getPath());

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

@@ -502,7 +502,7 @@ private Map<NimbleGenome, File> doAlignment(List<NimbleGenome> genomes, List<Fil
 
     public static void write10xBarcodes(File bam, Logger log, Readset rs, ReferenceGenome referenceGenome, PipelineStepOutput output) throws PipelineJobException
     {
-        // Write barcodes:
+        log.info("Writing 10x CB/UMIs to TSV");
         DISCVRSeqRunner runner = new DISCVRSeqRunner(log);
         List<String> barcodeArgs = new ArrayList<>(runner.getBaseArgs("Save10xBarcodes"));
         barcodeArgs.add("-I");