Do more cleanup in CellRangerVDJWrapper

Author: bbimber

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

@@ -419,6 +419,9 @@ public AlignmentStep.AlignmentOutput performAlignment(Readset rs, List<File> inp
                 getPipelineCtx().getLogger().warn("Unable to find folder: " + directory.getPath());
             }
 
+            output.addIntermediateFile(new File(outdir, "vdj_reference"));
+            output.addIntermediateFile(new File(outdir, "multi"));
+
             try
             {
                 File outputHtml = new File(outdir, "per_sample_outs/" + id + "/web_summary.html");
@@ -517,6 +520,19 @@ else if (isPrimaryDir)
                 output.addSequenceOutput(outputVloupe, rs.getName() + " 10x VLoupe", "10x VLoupe", rs.getRowId(), null, referenceGenome.getGenomeId(), versionString);
             }
 
+            output.addIntermediateFile(new File(sampleDir, "airr_rearrangement.tsv"));
+            output.addIntermediateFile(new File(sampleDir, "all_contig_annotations.bed"));
+            output.addIntermediateFile(new File(sampleDir, "all_contig_annotations.json"));
+            output.addIntermediateFile(new File(sampleDir, "cell_barcodes.json"));
+            output.addIntermediateFile(new File(sampleDir, "concat_ref.bam"));
+            output.addIntermediateFile(new File(sampleDir, "concat_ref.bam.bai"));
+            output.addIntermediateFile(new File(sampleDir, "concat_ref.fasta"));
+            output.addIntermediateFile(new File(sampleDir, "concat_ref.fasta.fai"));
+            output.addIntermediateFile(new File(sampleDir, "consensus.bam"));
+            output.addIntermediateFile(new File(sampleDir, "consensus.bam.bai"));
+            output.addIntermediateFile(new File(sampleDir, "donor_regions.fa"));
+            output.addIntermediateFile(new File(sampleDir, "vdj_contig_info.pb"));
+
             return csv;
         }