Pass nCores to UCell

Author: bbimber

singlecell/resources/chunks/CalculateUCellScores.R

@@ -1,9 +1,15 @@
+if (Sys.getenv('SEURAT_MAX_THREADS') != '') {
+    nCores <- Sys.getenv('SEURAT_MAX_THREADS')
+} else {
+    nCores <- 1
+}
+
 for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
     message(paste0('Loading dataset ', datasetId, ', with total cells: ', ncol(seuratObj)))
-    seuratObj <- RIRA::CalculateUCellScores(seuratObj, storeRanks = storeRanks, assayName = assayName, forceRecalculate = forceRecalculate)
+    seuratObj <- RIRA::CalculateUCellScores(seuratObj, storeRanks = storeRanks, assayName = assayName, forceRecalculate = forceRecalculate, ncores = nCores)
 
     saveData(seuratObj, datasetId)
 

singlecell/resources/chunks/CustomUCell.R

@@ -23,7 +23,13 @@ for (datasetId in names(seuratObjects)) {
     toCalculate[[vals[1]]] <- geneList
   }
 
-  seuratObj <- UCell::AddModuleScore_UCell(seuratObj, features = toCalculate, storeRanks = storeRanks, assay = assayName)
+  if (Sys.getenv('SEURAT_MAX_THREADS') != '') {
+    nCores <- Sys.getenv('SEURAT_MAX_THREADS')
+  } else {
+    nCores <- 1
+  }
+
+  seuratObj <- UCell::AddModuleScore_UCell(seuratObj, features = toCalculate, storeRanks = storeRanks, assay = assayName, ncores = nCores)
   corData <- RIRA::PlotUcellCorrelation(seuratObj, toCalculate)
 
   for (n in names(toCalculate)) {