cleaning + add option skip plot matrix

nextflow.config

@@ -93,6 +93,7 @@ params {
     skip_compartments = false
     skip_tads = false
     skip_multiqc = false
+    skip_plot_matrix = false
 
     // MultiQC options
     multiqc_config             = null

nextflow_schema.json

@@ -339,6 +339,10 @@
                 "skip_multiqc": {
                     "type": "boolean",
                     "description": "Do not generate MultiQC report"
+                },
+                "skip_plot_matrix": {
+                    "type": "boolean",
+                    "description": "Do not generate matrices"
                 }
             }
         },

workflows/hic.nf

@@ -41,12 +41,7 @@ if (params.digestion){
 //****************************************
 // Combine all maps resolution for downstream analysis
 
-/* 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){
@@ -223,10 +218,12 @@ workflow HIC {
   //
   // MODULE: HICEXPLORER/HIC_PLOT_MATRIX
   //
-  HIC_PLOT_MATRIX(
-    COOLER.out.cool
-  )
+  if (!params.skip_plot_matrix){
+    HIC_PLOT_MATRIX(
+        COOLER.out.cool
+    )
   ch_versions = ch_versions.mix(HIC_PLOT_MATRIX.out.versions)
+  }
 
   //
   // SUB-WORKFLOW: COMPARTMENT CALLING