[MODIF] test --skip_compartment option nf-core#125

Author: nservant

conf/modules.config

@@ -274,7 +274,7 @@ process {
             mode: 'copy'
         ]
         ext.args = '15 25 50 --window-pixels'
-	ext.prefix = { "${meta.id}.${resolution}" }
+	ext.prefix = { "${cool.baseName}" }
     }
 
     withName: 'HIC_FIND_TADS' {
@@ -284,6 +284,6 @@ process {
             mode: 'copy'
         ]
         ext.args = '--correctForMultipleTesting fdr'
-	ext.prefix = { "${meta.id}.${resolution}" }
+	ext.prefix = { "${cool.baseName}" }
     }
 }

nextflow.config

@@ -50,8 +50,8 @@ params {
          ligation_site='GATCGATC'
       }
       'arima' {
-         restriction_site='^GATC,G^ANT'
-         ligation_site='GATCGATC,GANTGATC,GANTANTC,GATCANTC'
+         restriction_site='^GATC,G^ANTC'
+         ligation_site='GATCGATC,GATCANTC,GANTGATC,GANTANTC'
       }
     }
 

workflows/hic.nf

@@ -67,7 +67,7 @@ if (params.res_dist_decay && !params.skip_dist_decay){
     .set {ch_ddecay_res}
    ch_map_res = ch_map_res.concat(ch_ddecay_res)
 }else{
-  ch_ddecay_res = Channel.create()
+  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" 
   }
@@ -81,7 +81,7 @@ if (params.res_compartments && !params.skip_compartments){
     .set {ch_comp_res}
    ch_map_res = ch_map_res.concat(ch_comp_res)
 }else{
-  ch_comp_res = Channel.create()
+  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" 
   }