diff --git a/workflow/conf/multiqc_config.yaml b/workflow/conf/multiqc_config.yaml
index 8b8a4d49a880f0f6b22fd55d3d9f52207aa1ba6a..30b6936b8b7997598ebde2df9afcee1076cd630e 100644
--- a/workflow/conf/multiqc_config.yaml
+++ b/workflow/conf/multiqc_config.yaml
@@ -46,6 +46,12 @@ top_modules:
       info: '1M Downsampled Reads Strandedness Inference Results'
       path_filters:
         - '*infer_experiment*'
+  - Software_Versions:
+      path_filters:
+        - 'software_versions_mqc.yaml'
+  - Software_References:
+      path_filters:
+        - 'software_references_mqc.yaml'
 
 
 report_section_order:
@@ -57,10 +63,6 @@ report_section_order:
       order: 2000
     ref:
       order: 1000
-    Software_Versions:
-      after: 'Inference: Stranded'
-    Software_References:
-      after: 'Software_Versions'
 
 
 skip_generalstats: true