Omit writing to 10x barcodes

Author: bbimber

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

@@ -88,8 +88,6 @@ 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/CellRangerGexCountStep.java

@@ -396,15 +396,6 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
         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);
-        }
-        else
-        {
-            getPipelineCtx().getLogger().info("BAM file does not exist, cannot write 10x barcodes: " + bam.getPath());
-        }
-
         if (!shouldDiscardBam())
         {
             if (!bam.exists())

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

@@ -41,7 +41,6 @@ public class NimbleAlignmentStep extends AbstractCellRangerDependentStep
     public static final String MAX_HITS_TO_REPORT = "maxHitsToReport";
     public static final String STRANDEDNESS = "strandedness";
     public static final String REQUIRE_CACHED_BARCODES = "requireCachedBarcodes";
-    public static final String WRITE_10X_BARCODES = "write10xBarcodes";
 
     public NimbleAlignmentStep(AlignmentStepProvider<?> provider, PipelineContext ctx, CellRangerWrapper wrapper)
     {
@@ -77,10 +76,7 @@ public static List<ToolParameterDescriptor> getToolParameters()
                 }}, 4),
                 ToolParameterDescriptor.create(REQUIRE_CACHED_BARCODES, "Fail Unless Cached Barcodes Present", "If checked, the pipeline will expect a previously computed map of cellbarcodes and UMIs to be computed. Under default conditions, if this is missing, cellranger will be re-run. This flag can be helpful to avoid that computation if you expect the barcode file to exist.", "checkbox", new JSONObject(){{
 
-                }}, false),
-                ToolParameterDescriptor.create(WRITE_10X_BARCODES, "Write 10x Barcodes To File", "If checked, the pipeline will save the 10x barcodes from the BAM to a TSV. This facilitates future analyses.", "checkbox", new JSONObject(){{
-
-                }}, true)
+                }}, false)
         );
     }
 

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

@@ -18,8 +18,6 @@
 import java.util.LinkedHashSet;
 import java.util.List;
 
-import static org.labkey.singlecell.run.NimbleAlignmentStep.WRITE_10X_BARCODES;
-
 public class NimbleAnalysis extends AbstractPipelineStep implements AnalysisStep
 {
     public NimbleAnalysis(PipelineStepProvider<?> provider, PipelineContext ctx)
@@ -60,16 +58,6 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
         NimbleHelper helper = new NimbleHelper(getPipelineCtx(), getProvider(), getStepIdx());
         helper.doNimbleAlign(inputBam, output, rs, FileUtil.getBaseName(inputBam));
 
-        boolean write10xBarcodes = getProvider().getParameterByName(WRITE_10X_BARCODES).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, true);
-        if (write10xBarcodes)
-        {
-            NimbleHelper.write10xBarcodes(inputBam, getPipelineCtx().getLogger(), rs, referenceGenome, output);
-        }
-        else
-        {
-            getPipelineCtx().getLogger().info("10x barcodes will not be saved to TSV");
-        }
-
         return output;
     }