Update AppendCiteSeq for newer versions

BimberLab · Aug 7, 2024 · 6545d95 · 6545d95
1 parent e285a64
commit 6545d95
Showing 1 changed file with 7 additions and 0 deletions.
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendCiteSeq.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendCiteSeq.java
@@ -132,7 +132,14 @@ protected Map<Integer, File> prepareCountData(SingleCellOutput output, SequenceO
 
                 if (dropAggregateBarcodes)
                 {
+                    // NOTE: this is the location in CellRanger <= 6.x
                     File aggregateCountFile = new File(existingCountMatrixUmiDir.getParentFile(), "antibody_analysis/aggregate_barcodes.csv");
+                    if (!aggregateCountFile.exists())
+                    {
+                        // This is the location for >= 7.x
+                        aggregateCountFile = new File(existingCountMatrixUmiDir.getParentFile(), "aggregate_barcodes.csv");
+                    }
+
                     if (!aggregateCountFile.exists())
                     {
                         throw new PipelineJobException("Unable to find aggregate count file: " + aggregateCountFile.getPath());