Bugfix to expectedDefaultAssay in merge

bbimber · bbimber · commit 7ab62f3a3b2d · 2026-01-28T16:03:50.000-08:00
diff --git a/singlecell/resources/chunks/MergeSeurat.R b/singlecell/resources/chunks/MergeSeurat.R
@@ -43,7 +43,7 @@ mergeBatchInMemory <- function(datasetIdToFilePath, saveFile) {
         stop('There were no passing seurat objects!')
     }
 
-    saveRDS(CellMembrane::MergeSeuratObjs(toMerge, projectName = projectName, doGC = doDiet, errorOnBarcodeSuffix = errorOnBarcodeSuffix), file = saveFile, expectedDefaultAssay = expectedDefaultAssay)
+    saveRDS(CellMembrane::MergeSeuratObjs(toMerge, projectName = projectName, doGC = doDiet, errorOnBarcodeSuffix = errorOnBarcodeSuffix, expectedDefaultAssay = expectedDefaultAssay), file = saveFile)
     filesToDelete <<- c(filesToDelete, saveFile)
 
     logger::log_info(paste0('mem used: ', R.utils::hsize(as.numeric(pryr::mem_used()))))

Original file line number	Diff line number	Diff line change
`@@ -43,7 +43,7 @@ mergeBatchInMemory <- function(datasetIdToFilePath, saveFile) {`
`43`	`43`	`stop('There were no passing seurat objects!')`
`44`	`44`	`}`
`45`	`45`
`46`		`- saveRDS(CellMembrane::MergeSeuratObjs(toMerge, projectName = projectName, doGC = doDiet, errorOnBarcodeSuffix = errorOnBarcodeSuffix), file = saveFile, expectedDefaultAssay = expectedDefaultAssay)`
	`46`	`+ saveRDS(CellMembrane::MergeSeuratObjs(toMerge, projectName = projectName, doGC = doDiet, errorOnBarcodeSuffix = errorOnBarcodeSuffix, expectedDefaultAssay = expectedDefaultAssay), file = saveFile)`
`47`	`47`	`filesToDelete <<- c(filesToDelete, saveFile)`
`48`	`48`
`49`	`49`	`logger::log_info(paste0('mem used: ', R.utils::hsize(as.numeric(pryr::mem_used()))))`