fix bug

main.nf

@@ -106,6 +106,7 @@ if (params.genomes && params.genome && !params.genomes.containsKey(params.genome
 if (params.digest && params.digestion && !params.digest.containsKey(params.digestion)) {
    exit 1, "Unknown digestion protocol. Currently, the available digestion options are ${params.digest.keySet().join(", ")}. Please set manually the '--restriction_site' and '--ligation_site' parameters."
 }
+
 params.restriction_site = params.digestion ? params.digest[ params.digestion ].restriction_site ?: false : false
 params.ligation_site = params.digestion ? params.digest[ params.digestion ].ligation_site ?: false : false
 

nextflow.config

@@ -17,10 +17,6 @@ params {
   restriction_fragments = false
   save_reference = false
  
-  // Dnase Hi-C
-  dnase = false
-  min_cis_dist = 0
-
   // Mapping
   split_fastq = false
   fastq_chunks_size = 20000000
@@ -34,14 +30,7 @@ params {
 
 
   // Digestion Hi-C
-  digestion = 'hindiii'
-  restriction_site = ''
-  ligation_site = ''
-  min_restriction_fragment_size = 0
-  max_restriction_fragment_size = 0
-  min_insert_size = 0
-  max_insert_size =0
-
+  digestion = false
   digest {
     'hindiii'{
        restriction_site='A^AGCTT'
@@ -60,6 +49,10 @@ params {
        ligation_site='GATCGATC,GATCGANT,GANTGATC,GANTGANT'
     }
   }
+  min_restriction_fragment_size = 0
+  max_restriction_fragment_size = 0
+  min_insert_size = 0
+  max_insert_size = 0
 
   // Dnase Hi-C
   dnase = false