Bugfix to SubsetSeurat when a downstream filter returns zero cells

Author: bbimber

jbrowse/src/org/labkey/jbrowse/JBrowseMaintenanceTask.java

@@ -179,7 +179,7 @@ private void processContainer(Container c, Logger log) throws IOException
             User u = LDKService.get().getBackgroundAdminUser();
             if (u == null)
             {
-                log.error("In order to ensure genomes are prepared for JBrowse, the LDK module property BackgroundAdminUser must be set");
+                log.warn("In order to ensure genomes are prepared for JBrowse, the LDK module property BackgroundAdminUser must be set");
             }
             else
             {

singlecell/resources/chunks/SubsetSeurat.R

@@ -7,8 +7,13 @@ for (datasetId in names(seuratObjects)) {
 		seuratObj$HTO.Classification <- seuratObj$consensuscall.global
 	}
 
+	print(paste0('Initial cells for dataset: ', datasetId, ' ', ncol(seuratObj)))
 	<SUBSET_CODE>
 
+	if (!is.null(seuratObj)) {
+		newSeuratObjects[[datasetId]] <- seuratObj
+	}
+
 	# Cleanup
 	rm(seuratObj)
 	gc()

singlecell/src/org/labkey/singlecell/pipeline/singlecell/SubsetSeurat.java

@@ -81,6 +81,7 @@ protected List<String> loadChunkFromFile() throws PipelineJobException
                     String subsetEscaped = subset.replace("'", "\\\'");
 
                     ret.add("\tif (!is.null(seuratObj)) {");
+                    ret.add("\tprint(paste0('Subsetting dataset: ', datasetId, ' with the expression: '" + subsetEscaped + "'))");
                     ret.add("\t\tcells <- c()");
                     ret.add("\t\ttryCatch({");
                     ret.add("\t\t\tcells <- WhichCells(seuratObj, expression = " + subset + ")");
@@ -96,9 +97,9 @@ protected List<String> loadChunkFromFile() throws PipelineJobException
                     ret.add("\t\t} else {");
                     ret.add("\t\t\tseuratObj <- subset(seuratObj, cells = cells)");
                     ret.add("\t\t\tprint(paste0('Cells after subset: ', ncol(seuratObj)))");
-                    ret.add("\t\t\tnewSeuratObjects[[datasetId]] <- seuratObj");
                     ret.add("\t\t}");
-                    ret.add("}");
+                    ret.add("\t}");
+                    ret.add("");
                 }
             }
             else