diff --git a/workflow/conf/multiqc_config.yaml b/workflow/conf/multiqc_config.yaml
index 51b196d40f4e46a82a36f0156503c42c6432aebc..52e7cec1addf3221ab629a10ddce86f10532f323 100644
--- a/workflow/conf/multiqc_config.yaml
+++ b/workflow/conf/multiqc_config.yaml
@@ -54,3 +54,9 @@ table_columns_visible:
     Reads Mapped Confidently to Exonic Regions: False
 
 thousandsSep_format: ''
+
+report_section_order:
+    Software_Versions:
+      order: -1100
+    Software_References:
+      order: -1200
diff --git a/workflow/main.nf b/workflow/main.nf
index 44ae660f36bf5dbee5a3bf20ad4850a7b8bff04e..79895ef9861c3a99dd0791c2599e95e276946038 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -56,7 +56,7 @@ forceCells = params.forceCells
 chemistryParam = params.chemistryParam
 version = params.version
 outDir = params.outDir
-multiqcConf = params.multiqc
+multiqcConf = params.multiqcConf
 references = params.references
 
 
@@ -286,6 +286,6 @@ process multiqc {
   ulimit -a
   awk 'FNR==1 && NR!=1{next;}{print}' *.tsv > metrics_summary_mqc.tsv
   sed -i '1s/^.*\tE/Sample\tE/' metrics_summary_mqc.tsv
-  multiqc -c $multiqcConf
+  multiqc -c $multiqcConf .
   """
 }