@@ -51,14 +51,15 @@ exportSCEtoAnnData <- function(sce,

   if (!is(SummarizedExperiment::assay(sce), 'dgCMatrix')) {

     SummarizedExperiment::assay(sce) <- .convertToMatrix(SummarizedExperiment::assay(sce))

   }

-

+  

+  dir.create(outputDir, showWarnings = FALSE, recursive = TRUE)

   annData <- .sce2adata(sce,useAssay)

   fileName <- paste0(sample,".h5ad")

   filePath <- file.path(outputDir,fileName)

-  

+

   if (file.exists(filePath) && !isTRUE(overwrite)) {

     stop(paste0(path, " already exists. Change 'outputDir' or set 'overwrite' to TRUE."))

-    }

+  }

   annData$write_h5ad(filePath,

                      compression = compression,