Support tool to write 10x barcodes to file

Author: bbimber

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

@@ -87,6 +87,8 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
             }
         }
 
+        NimbleHelper.write10xBarcodes(localBam, getWrapper().getLogger(), rs, referenceGenome, output);
+
         // Now run nimble itself:
         NimbleHelper helper = new NimbleHelper(getPipelineCtx(), getProvider(), getStepIdx());
         helper.doNimbleAlign(localBam, output, rs, basename);

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

@@ -58,6 +58,8 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
         NimbleHelper helper = new NimbleHelper(getPipelineCtx(), getProvider(), getStepIdx());
         helper.doNimbleAlign(inputBam, output, rs, FileUtil.getBaseName(inputBam));
 
+        NimbleHelper.write10xBarcodes(inputBam, getPipelineCtx().getLogger(), rs, referenceGenome, output);
+
         return output;
     }
 

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

@@ -5,6 +5,7 @@
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.io.output.StringBuilderWriter;
 import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONArray;
 import org.json.JSONObject;
@@ -27,6 +28,7 @@
 import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
+import org.labkey.api.sequenceanalysis.run.DISCVRSeqRunner;
 import org.labkey.api.sequenceanalysis.run.DockerWrapper;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.writer.PrintWriters;
@@ -494,6 +496,28 @@ private Map<NimbleGenome, File> doAlignment(List<NimbleGenome> genomes, List<Fil
         return resultMap;
     }
 
+    public static void write10xBarcodes(File bam, Logger log, Readset rs, ReferenceGenome referenceGenome, PipelineStepOutput output) throws PipelineJobException
+    {
+        // Write barcodes:
+        DISCVRSeqRunner runner = new DISCVRSeqRunner(log);
+        List<String> barcodeArgs = new ArrayList<>(runner.getBaseArgs("Save10xBarcodes"));
+        barcodeArgs.add("--bam");
+        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());
+
+        runner.execute(barcodeArgs);
+
+        output.addSequenceOutput(cbOutput, "10x CellBarcode Map: " + rs.getName(), "10x CellBarcode Map", rs.getReadsetId(), null, referenceGenome.getGenomeId(), null);
+        output.addSequenceOutput(umiOutput, "10x UMI Map: " + rs.getName(), "10x UMI Map", rs.getReadsetId(), null, referenceGenome.getGenomeId(), null);
+    }
+
     public static File runNimbleReport(File alignResultsGz, int genomeId, PipelineStepOutput output, PipelineContext ctx) throws PipelineJobException
     {
         List<String> reportArgs = new ArrayList<>();