simplify int check and function for channel check

lib/WorkflowHic.groovy

@@ -3,7 +3,9 @@
 //
 
 import nextflow.Nextflow
+import nextflow.Channel
 import groovy.text.SimpleTemplateEngine
+import groovyx.gpars.dataflow.DataflowWriteChannel
 
 class WorkflowHic {
 
@@ -90,13 +92,19 @@ class WorkflowHic {
 
     // Check the params 'list of Integer' or Integer (ex bin_size)
     public static void checkParamIntList(def param2check, log) {
-        if (param2check instanceof Integer || (param2check instanceof String && param2check ==~ /(\d+)(,\d+)*/)){
-            //good format, do nothing
-        }
-        else {
-            println "\n"
+        if (param2check !instanceof Integer && !(param2check instanceof String && param2check ==~ /(\d+)(,\d+)*/)){            println "\n"
             log.error "ERROR: ${param2check} must be integer or list of integer"
             Nextflow.error('Exiting!')
         }
     }
+
+    // In hic.nf: check if the param is int. If true, don't splitCsv and flatten to avoid error
+    public static DataflowWriteChannel checkIfInt(def param2check) {
+        if (param2check instanceof Integer) {
+            return Channel.from( param2check ).toInteger()
+        }
+        else {
+            return Channel.from( param2check ).splitCsv().flatten().toInteger()
+        }
+    }
 }

workflows/hic.nf

@@ -41,23 +41,21 @@ if (params.digestion){
 //****************************************
 // Combine all maps resolution for downstream analysis
 
-if (params.bin_size instanceof Integer) {
+/* if (params.bin_size instanceof Integer) {
     ch_map_res = Channel.from( params.bin_size ).toInteger()
 }
 else {
     ch_map_res = Channel.from( params.bin_size ).splitCsv().flatten().toInteger()
-}
+} */
+ch_map_res = WorkflowHic.checkIfInt(params.bin_size)
 
 if (params.res_zoomify){
   ch_zoom_res = Channel.from( params.res_zoomify ).splitCsv().flatten().toInteger()
   ch_map_res = ch_map_res.concat(ch_zoom_res)
 }
 
-if (params.res_tads && !params.skip_tads && params.res_tads instanceof Integer){
-  ch_tads_res = Channel.from( "${params.res_tads}" ).toInteger()
-  ch_map_res = ch_map_res.concat(ch_tads_res)
-}else if (params.res_tads && !params.skip_tads){
-  ch_tads_res = Channel.from( "${params.res_tads}" ).splitCsv().flatten().toInteger()
+if (params.res_tads && !params.skip_tads){
+  ch_tads_res = WorkflowHic.checkIfInt(params.res_tads)
   ch_map_res = ch_map_res.concat(ch_tads_res)
 }else{
   ch_tads_res=Channel.empty()
@@ -66,11 +64,8 @@ if (params.res_tads && !params.skip_tads && params.res_tads instanceof Integer){
   }
 }
 
-if (params.res_dist_decay && !params.skip_dist_decay && params.res_dist_decay instanceof Integer){
-  ch_ddecay_res = Channel.from( "${params.res_dist_decay}" ).toInteger()
-  ch_map_res = ch_map_res.concat(ch_ddecay_res)
-}else if (params.res_dist_decay && !params.skip_dist_decay){
-  ch_ddecay_res = Channel.from( "${params.res_dist_decay}" ).splitCsv().flatten().toInteger()
+if (params.res_dist_decay && !params.skip_dist_decay){
+  ch_ddecay_res = WorkflowHic.checkIfInt(params.res_dist_decay)
   ch_map_res = ch_map_res.concat(ch_ddecay_res)
 }else{
   ch_ddecay_res = Channel.empty()
@@ -79,11 +74,8 @@ if (params.res_dist_decay && !params.skip_dist_decay && params.res_dist_decay in
   }
 }
 
-if (params.res_compartments && !params.skip_compartments && params.res_compartments instanceof Integer){
-  ch_comp_res = Channel.from( "${params.res_compartments}" ).toInteger()
-  ch_map_res = ch_map_res.concat(ch_comp_res)
-}else if (params.res_compartments && !params.skip_compartments){
-  ch_comp_res = Channel.from( "${params.res_compartments}" ).splitCsv().flatten().toInteger()
+if (params.res_compartments && !params.skip_compartments){
+  ch_comp_res = WorkflowHic.checkIfInt(params.res_compartments)
   ch_map_res = ch_map_res.concat(ch_comp_res)
 }else{
   ch_comp_res = Channel.empty()