Add run_krona option to allow skipping Krona chart creation

conf/test.config

@@ -37,6 +37,7 @@ params {
     run_metaphlan3                        = true
     run_centrifuge                        = true
     run_diamond                           = true
+    run_krona                             = true
     malt_save_reads                       = true
     kraken2_save_reads                    = true
     centrifuge_save_reads                 = true

conf/test_nopreprocessing.config

@@ -37,6 +37,7 @@ params {
     run_metaphlan3                        = true
     run_centrifuge                        = true
     run_diamond                           = true
+    run_krona                             = true
 }
 
 process {

nextflow.config

@@ -125,6 +125,9 @@ params {
     run_diamond                = false
     diamond_output_format      = 'tsv'  // TSV is only format with taxonomic information apparently
     diamond_save_reads         = false // this will override default diamond output format so no taxonomic profile is generated!
+
+    // krona
+    run_krona                  = false
 }
 
 // Load base.config by default for all pipelines

nextflow_schema.json

@@ -433,6 +433,9 @@
         },
         "diamond_save_reads": {
             "type": "boolean"
+        },
+        "run_krona": {
+            "type": "boolean"
         }
     }
 }

workflows/taxprofiler.nf

@@ -213,8 +213,10 @@ workflow TAXPROFILER {
     /*
         SUBWORKFLOW: VISUALIZATION_KRONA
     */
-    VISUALIZATION_KRONA ( PROFILING.out.profiles )
+    if ( params.run_krona ) {
-    ch_versions = ch_versions.mix( VISUALIZATION_KRONA.out.versions )
+        VISUALIZATION_KRONA ( PROFILING.out.profiles )
+        ch_versions = ch_versions.mix( VISUALIZATION_KRONA.out.versions )
+    }
 
     /*
         MODULE: MultiQC