Drop cellBender support

BimberLab · Apr 10, 2024 · 5d29ff0 · 5d29ff0
1 parent b22a685
commit 5d29ff0
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Showing 3 changed files with 1 addition and 10 deletions.
diff --git a/singlecell/resources/chunks/AppendCiteSeq.R b/singlecell/resources/chunks/AppendCiteSeq.R
@@ -24,7 +24,7 @@ for (datasetId in names(seuratObjects)) {
             }
         }
 
-        seuratObj <- CellMembrane::AppendCiteSeq(seuratObj, unfilteredMatrixDir = matrixDir, normalizeMethod = normalizeMethod, datasetId = datasetId, featureMetadata = featureMetadata, adtWhitelist = adtWhitelist, runCellBender = runCellBender, aggregateBarcodeFile = aggregateBarcodeFile)
+        seuratObj <- CellMembrane::AppendCiteSeq(seuratObj, unfilteredMatrixDir = matrixDir, normalizeMethod = normalizeMethod, datasetId = datasetId, featureMetadata = featureMetadata, adtWhitelist = adtWhitelist, aggregateBarcodeFile = aggregateBarcodeFile)
     } else {
         print('matrixDir was NULL, skipping CITE-seq')
     }

diff --git a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java
@@ -1107,11 +1107,6 @@ else if ("NotUsed".equals(val))
             descriptions.add("Cite-seq Normalization: " + citeNormalize);
         }
 
-        if (ctx.getParams().optBoolean("singleCell.AppendCiteSeq.runCellBender", false))
-        {
-            descriptions.add("Cite-seq/CellBender: true");
-        }
-
         return StringUtils.join(descriptions, "\n");
     }
 }
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendCiteSeq.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendCiteSeq.java
@@ -54,10 +54,6 @@ private static List<ToolParameterDescriptor> getParams()
             put("initialValues", "clr");
         }}, "clr"));
 
-        ret.add(SeuratToolParameter.create("runCellBender", "Run CellBender", "If checked, cellbender will be run on the raw count matrix to remove background/ambient RNA signal", "checkbox", new JSONObject(){{
-
-        }}, false));
-
         ret.add(SeuratToolParameter.create("dropAggregateBarcodes", "Drop Aggregate Barcodes", "If checked, any barcodes marked as protein aggregates by cellranger will be dropped.", "checkbox", new JSONObject(){{
             put("checked", true);
         }}, true));