diff --git a/wdl/cellbender_remove_background.wdl b/wdl/cellbender_remove_background.wdl
index 6f97463..f7507ec 100644
--- a/wdl/cellbender_remove_background.wdl
+++ b/wdl/cellbender_remove_background.wdl
@@ -125,8 +125,15 @@ task run_cellbender_remove_background_gpu {
             [ -f $dir/$name ] || mv ~{genes_file} $dir/$name
         fi
 
+        # use the directory as the input in the case of an MTX file
+        if [[ "~{input_file_unfiltered}" == *.mtx* ]]; then
+            input=$(dirname ~{input_file_unfiltered})
+        else
+            input=~{input_file_unfiltered}
+        fi
+
         cellbender remove-background \
-            --input "~{input_file_unfiltered}" \
+            --input $input \
             --output "~{sample_name}_out.h5" \
             --cuda \
             ~{"--checkpoint " + checkpoint_file} \