diff --git a/src/multiqc/config.vsh.yaml b/src/multiqc/config.vsh.yaml
index 7f29d109..0a3a784b 100644
--- a/src/multiqc/config.vsh.yaml
+++ b/src/multiqc/config.vsh.yaml
@@ -161,6 +161,12 @@ argument_groups:
         type: boolean_true
         description: |
           Disable coloured log output.
+      - name: "--cl_config"
+        type: string
+        required: false
+        description: |
+          YAML formatted string that allows to customize MultiQC behaviour like input file detection.
+        example: "qualimap_config: { general_stats_coverage: [20,40,200] }"
 
   - name: "Output format"
     arguments:
diff --git a/src/multiqc/script.sh b/src/multiqc/script.sh
index 6b04ff5b..b765520b 100755
--- a/src/multiqc/script.sh
+++ b/src/multiqc/script.sh
@@ -99,6 +99,7 @@ multiqc \
     ${include_modules} \
     ${par_include_modules:+--include-modules "$par_include_modules"} \
     ${par_data_format:+--data-format "$par_data_format"} \
+    ${par_cl_config:+--cl-config "$par_cl_config"} \
     ${par_zip_data_dir:+--zip-data-dir} \
     ${par_pdf:+--pdf} \
     ${par_interactive:+--interactive} \