Lint with new template

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

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

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",