Param validation

conf/test.config

@@ -38,5 +38,5 @@ params {
     res_compartments = '2000'
 
     // Ignore `--input` as otherwise the parameter validation will throw an error
-    schema_ignore_params = 'genomes,digest,input_paths,input'
+    schema_ignore_params = 'genomes,digest,input_paths,input,bin_size,res_dist_decay,res_tads,res_compartments'
 }

conf/test_full.config

@@ -24,4 +24,7 @@ params {
     bin_size = '40000,250000,500000,1000000'
     res_compartments = '500000,250000'
     res_tads = '40000,20000'
+
+    //Ignore parameters with special validation
+    schema_ignore_params = 'bin_size,res_dist_decay,res_tads,res_compartments'
 }

lib/WorkflowHic.groovy

@@ -3,7 +3,9 @@
 //
 
 import nextflow.Nextflow
+import nextflow.Channel
 import groovy.text.SimpleTemplateEngine
+import groovyx.gpars.dataflow.DataflowWriteChannel
 
 class WorkflowHic {
 
@@ -18,6 +20,11 @@ class WorkflowHic {
             Nextflow.error "Unknown digestion protocol. Currently, the available digestion options are ${params.digest.keySet().join(", ")}. Please set manually the '--restriction_site' and '--ligation_site' parameters."
         }
 
+        checkParamIntList(params.bin_size, log)
+        checkParamIntList(params.res_dist_decay, log)
+        checkParamIntList(params.res_tads, log)
+        checkParamIntList(params.res_compartments, log)
+
         // Check Digestion or DNase Hi-C mode
         //if (!params.dnase && !params.ligation_site) {
         //  Nextflow.error "Ligation motif not found. Please either use the `--digestion` parameters or specify the `--restriction_site` and `--ligation_site`. For DNase Hi-C, please use '--dnase' option"
@@ -82,4 +89,23 @@ class WorkflowHic {
             Nextflow.error(error_string)
         }
     }
+
+        // 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+)*/)){
+            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()
+        }
+    }
 }

nextflow.config

@@ -110,7 +110,7 @@ params {
     version                    = false
     validate_params            = true
     show_hidden_params         = false
-    schema_ignore_params       = 'genomes,digest'
+    schema_ignore_params       = 'genomes,digest,bin_size,res_dist_decay,res_tads,res_compartments'
 
     // Config options
     custom_config_version      = 'master'

workflows/hic.nf

@@ -41,40 +41,40 @@ if (params.digestion){
 //****************************************
 // Combine all maps resolution for downstream analysis
 
-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){
-  ch_tads_res = Channel.from( "${params.res_tads}" ).splitCsv().flatten().toInteger()
+  ch_tads_res = WorkflowHic.checkIfInt(params.res_tads)
   ch_map_res = ch_map_res.concat(ch_tads_res)
 }else{
   ch_tads_res=Channel.empty()
   if (!params.skip_tads){
-    log.warn "[nf-core/hic] Hi-C resolution for TADs calling not specified. See --res_tads" 
+    log.warn "[nf-core/hic] Hi-C resolution for TADs calling not specified. See --res_tads"
   }
 }
 
 if (params.res_dist_decay && !params.skip_dist_decay){
-  ch_ddecay_res = Channel.from( "${params.res_dist_decay}" ).splitCsv().flatten().toInteger()
+  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()
   if (!params.skip_dist_decay){
-    log.warn "[nf-core/hic] Hi-C resolution for distance decay not specified. See --res_dist_decay" 
+    log.warn "[nf-core/hic] Hi-C resolution for distance decay not specified. See --res_dist_decay"
   }
 }
 
 if (params.res_compartments && !params.skip_compartments){
-  ch_comp_res = Channel.from( "${params.res_compartments}" ).splitCsv().flatten().toInteger()
+  ch_comp_res = WorkflowHic.checkIfInt(params.res_compartments)
   ch_map_res = ch_map_res.concat(ch_comp_res)
 }else{
   ch_comp_res = Channel.empty()
   if (!params.skip_compartments){
-    log.warn "[nf-core/hic] Hi-C resolution for compartment calling not specified. See --res_compartments" 
+    log.warn "[nf-core/hic] Hi-C resolution for compartment calling not specified. See --res_compartments"
   }
 }
 
@@ -99,7 +99,7 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil
 //
 // MODULE: Local to the pipeline
 //
-include { HIC_PLOT_DIST_VS_COUNTS } from '../modules/local/hicexplorer/hicPlotDistVsCounts' 
+include { HIC_PLOT_DIST_VS_COUNTS } from '../modules/local/hicexplorer/hicPlotDistVsCounts'
 include { MULTIQC } from '../modules/local/multiqc'
 
 //
@@ -239,7 +239,7 @@ workflow HIC {
       .filter{ it[0].resolution == it[2] }
       .map { it -> [it[0], it[1]]}
       .set{ ch_cool_tads }
-                                                                                                                                                                                                            
+
     TADS(
       ch_cool_tads
     )