diff --git a/bin/add_celltypes_to_sce.R b/bin/add_celltypes_to_sce.R
index 7a16c434..4531f78e 100755
--- a/bin/add_celltypes_to_sce.R
+++ b/bin/add_celltypes_to_sce.R
@@ -22,7 +22,7 @@ option_list <- list(
     help = "path to output rds file to store annotated sce object. Must end in .rds"
   ),
   make_option(
-    opt_str = c("singler_results"),
+    opt_str = c("--singler_results"),
     type = "character",
     help = "path to rds file containing SingleR results object"
   ),
@@ -34,7 +34,7 @@ option_list <- list(
   make_option(
     opt_str = c("--cellassign_ref_name"),
     type = "character",
-    help = "Name of reference used for CellAssign"
+    help = "name of reference used for CellAssign"
   )
 )
 
@@ -109,6 +109,7 @@ if(!is.null(opt$cellassign_predictions)){
   
   predictions <- readr::read_tsv(opt$cellassign_predictions)
   
+  # get cell type with maximum prediction value for each cell
   celltype_assignments <- predictions |>
     tidyr::pivot_longer(
       !barcode,
diff --git a/modules/classify-celltypes.nf b/modules/classify-celltypes.nf
index 16fdc132..d3e9b104 100644
--- a/modules/classify-celltypes.nf
+++ b/modules/classify-celltypes.nf
@@ -93,24 +93,26 @@ process add_celltypes_to_sce {
   input:
     tuple val(meta), path(processed_rds), path(singler_dir), path(cellassign_dir)
   output:
-    tuple val(meta), path(processed_rds)
+    tuple val(meta), path(annotated_rds)
   script:
+    annotated_rds = "${meta.library_id}_processed_annotated.rds"
     singler_present = "${singler_dir.name}" != "NO_FILE"
     singler_results = "${singler_dir}/singler_results.rds"
     cellassign_present = "${cellassign_dir}.name" != "NO_FILE"
     cellassign_predictions = "${cellassign_dir}/cellassign_predictions.tsv"
-    cellassign_ref_name = file("${meta.cellassign_reference_file}").name
+    cellassign_ref_name = file("${meta.cellassign_reference_file}").baseName
     """
     add_celltypes_to_sce.R \
       --input_sce_file ${processed_rds} \
-      --output_sce_file ${processed_rds} \
+      --output_sce_file ${annotated_rds} \
       ${singler_present ? "--singler_results  ${singler_results}" : ''} \
       ${cellassign_present ? "--cellassign_predictions  ${cellassign_predictions}" : ''} \
       ${cellassign_present ? "--cellassign_ref_name ${cellassign_ref_name}" : ''}
     """
   stub:
+    annotated_rds = "${meta.library_id}_processed_annotated.rds"
     """
-    touch ${processed_rds}
+    touch ${annotated_rds}
     """
 }
 
@@ -209,10 +211,15 @@ workflow annotate_celltypes {
 
       // incorporate annotations into SCE object
       add_celltypes_to_sce(assignment_input_ch.add_celltypes)
+      
+      // mix in libraries without new celltypes
+      // result is [meta, proccessed rds]
+      celltyped_ch = assignment_input_ch.no_celltypes
+        .map{[it[0], it[1]]}
+        .mix(add_celltypes_to_sce.out) 
 
       // add back in the unchanged sce files to the results
-      export_channel = add_celltypes_to_sce.out
-        .mix(assignment_input_ch.no_celltypes.map{[it[0], it[1]]})
+      export_channel = celltyped_ch
         .map{[it[0]["library_id"]] + it}
         // add in unfiltered and filtered sce files
         .join(sce_files_channel.map{[it[0]["library_id"], it[1], it[2]]},