diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 074bbba..e647ad5 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -13,4 +13,6 @@ report_section_order:
 export_plots: true
 
 disable_version_detection: true
-prokka_fn_snames: True
+use_filename_as_sample_name:
+  - prokka
+  - bakta