diff --git a/conf/modules/align_reads.config b/conf/modules/align_reads.config
index ea3cb56f..bdc17134 100644
--- a/conf/modules/align_reads.config
+++ b/conf/modules/align_reads.config
@@ -31,9 +31,9 @@ process {
 
     withName: MINIMAP2_ALIGN_UNSPLIT {
         if(params.preset == 'revio' | params.preset == 'pacbio') {
-            ext.args = "-y -x map-hifi --secondary=no"
+            ext.args = "-y -x map-hifi --secondary=no -Y"
         } else if(params.preset == 'ONT_R9' | params.preset == 'ONT_R10') {
-            ext.args = "-y -x map-ont --secondary=no"
+            ext.args = "-y -x map-ont --secondary=no -Y"
         }
 
         publishDir = [
@@ -54,9 +54,9 @@ process {
 
     withName: MINIMAP2_ALIGN_SPLIT {
         if(params.preset == 'revio' | params.preset == 'pacbio') {
-            ext.args = "-y -x map-hifi --secondary=no"
+            ext.args = "-y -x map-hifi --secondary=no -Y"
         } else if(params.preset == 'ONT_R9' | params.preset == 'ONT_R10') {
-            ext.args = "-y -x map-ont --secondary=no"
+            ext.args = "-y -x map-ont --secondary=no -Y"
         }
         // Not part of preprocessing workflow now but makes sense to store it there
         publishDir = [