diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 71b56fd..e6f1a85 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -39,6 +39,10 @@ sp:
   diamond:
     contents: "diamond v"
     num_lines: 10
+  fastqc/data:
+    fn_re: ".*[fastqc|falco]_data.txt"
+  fastqc/zip:
+    fn: "*_fastqc.zip"
 
 #extra_fn_clean_exts:
 #    - '_fastp'
@@ -49,11 +53,17 @@ top_modules:
   - "fastqc":
       name: "FastQC (pre-Trimming)"
       path_filters:
-        - "*raw_*fastqc.zip"
+        - "*raw*"
+      path_filters_exclude:
+        - "*falco*"
+        - "*processed*"
   - "fastqc":
       name: "Falco (pre-Trimming)"
       path_filters:
-        - "*_raw_falco_*_report.html"
+        - "*raw*"
+        - "*[falco]*"
+      path_filters_exclude:
+        - "*processed*"
   - "fastp"
   - "adapterRemoval"
   - "porechop":
@@ -61,11 +71,17 @@ top_modules:
   - "fastqc":
       name: "FastQC (post-Trimming)"
       path_filters:
-        - "*_processed_*fastqc.zip"
+        - "*processed*"
+      path_filters_exclude:
+        - "*falco*"
+        - "*raw*"
   - "fastqc":
       name: "Falco (post-Trimming)"
       path_filters:
-        - "*_processed_falco_*_report.html"
+        - "*processed*"
+        - "*falco*"
+      path_filters_exclude:
+        - "*raw*"
   - "bbduk"
   - "prinseqplusplus"
   - "filtlong"