diff --git a/main.nf b/main.nf
index 0cfcbc67001461bd73d04d497056d11387c722aa..5f7e943327ce8163c0c6c1bc373e97c02b864907 100644
--- a/main.nf
+++ b/main.nf
@@ -244,6 +244,7 @@ summary['Restriction Motif']= params.restriction_site
 summary['Ligation Motif']   = params.ligation_site
 summary['DNase Mode']       = params.dnase
 summary['Remove Dup']       = params.rm_dup
+summary['Remove MultiHits'] = params.rm_multi
 summary['Min MAPQ']         = params.min_mapq
 summary['Min Fragment Size']= params.min_restriction_fragment_size
 summary['Max Fragment Size']= params.max_restriction_fragment_size
diff --git a/nextflow.config b/nextflow.config
index c598df934ea0bd8b61c414117332211b792a99f8..edb8038b95bffe88773574849a2ce4df07e9aec4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -39,9 +39,10 @@ params {
   min_insert_size = false
   max_insert_size = false
   dnase = false
-  rm_dup = false
-  rm_singleton = false
-  rm_multi = false
+  min_cis_dist = false
+  rm_dup = true
+  rm_singleton = true
+  rm_multi = true
   bin_size = '1000000,500000'
   ice_max_iter = 100
   ice_filer_low_count_perc = 0.02
diff --git a/nextflow_schema.json b/nextflow_schema.json
index bb4529597d769dc9e5b74ceed8ebcd2567b5ac8a..ed2f701f6d62f11b45df12a035594bec31401d5e 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -132,15 +132,18 @@
                 },
                 "rm_dup": {
                     "type": "boolean",
-                    "description": "Remove duplicates"
+                    "description": "Remove duplicates",
+                    "default": true
                 },
                 "rm_multi": {
                     "type": "boolean",
-                    "description": "Remove multi-mapped reads"
+                    "description": "Remove multi-mapped reads",
+                    "default": true
                 },
                 "rm_singleton": {
                     "type": "boolean",
-                    "description": "Remove singleton"
+                    "description": "Remove singleton",
+                    "default": true
                 },
                 "min_mapq": {
                     "type": "integer",