Try putting MillironX's krona in subworkflow

conf/modules.config

@@ -293,7 +293,16 @@ process {
         ]
     }
 
-    withName: KRONA_IMPORTKRAKEN {
+    withName: KRAKENTOOLS_KREPORT2KRONA {
+        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+    }
+
+    withName: KRONA_KRAKENCLEANUP {
+        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+    }
+
+    withName: KRONA_KTIMPORTTEXT {
+        ext.prefix = { "${meta.tool}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/krona" },
             mode: params.publish_dir_mode,

subworkflows/local/postprocessing_krona.nf

@@ -0,0 +1,66 @@
+//
+// Remove host reads via alignment and export off-target reads
+//
+
+include { KRAKENTOOLS_KREPORT2KRONA                } from '../../modules/nf-core/modules/krakentools/kreport2krona/main'
+include { KRONA_CLEANUP as KRONA_KRAKENCLEANUP     } from '../../modules/local/krona_cleanup'
+include { KRONA_KTIMPORTTEXT                       } from '../../modules/nf-core/modules/krona/ktimporttext/main'
+include { CENTRIFUGE_KREPORT                       } from '../../modules/nf-core/modules/centrifuge/kreport/main'
+
+workflow POSTPROCESSING_KRONA {
+    take:
+    krona_input
+    databases
+
+    main:
+    ch_versions               = Channel.empty()
+    ch_input_for_ktimporttext = Channel.empty()
+
+    ch_files_for_krona = krona_input
+        .branch {
+            // malt:
+            kraken2: it[0]['tool'] == 'kraken2'
+            centrifuge:  it[0]['tool'] == 'centrifuge'
+            //metaphlan3:
+            //kaiju:
+            //diamond:
+        }
+
+    ch_databases = databases
+        .branch{
+            centrifuge: it[0]['tool'] == 'centrifuge'
+        }
+
+    // TODO PUSH BACK CENTRIFUGE_KREPORT TO PROFILING.NF WHERE DATABASE ALREADY IS?
+    ch_input_for_centrifuge_kreport = ch_files_for_krona.centrifuge
+                                        .dump(tag: "db_for_kreport_pre")
+                                        .join(ch_databases, by: 0)
+                                        .dump(tag: "db_for_kreport_post")
+
+
+    // Kraken
+    KRAKENTOOLS_KREPORT2KRONA ( ch_files_for_krona.kraken2 )
+    KRONA_KRAKENCLEANUP ( KRAKENTOOLS_KREPORT2KRONA.out.txt )
+    ch_kraken_for_krona = KRONA_KRAKENCLEANUP.out.txt
+                            .map{
+                                    [[id: it[0].tool + "-" + it[0].db_name, db_name: it[0].db_name, tool: it[0].tool ], it[1]]
+                                }
+                                .groupTuple()
+    ch_input_for_ktimporttext = ch_input_for_ktimporttext.mix( ch_kraken_for_krona )
+    ch_versions               = ch_versions.mix( KRAKENTOOLS_KREPORT2KRONA.out.versions.first() )
+    ch_versions               = ch_versions.mix( KRONA_KRAKENCLEANUP.out.versions.first() )
+
+
+    KRONA_KTIMPORTTEXT (ch_input_for_ktimporttext)
+
+
+    ch_versions        = ch_versions.mix( KRONA_KTIMPORTTEXT.out.versions.first() )
+
+    // Centrifuge
+    //CENTRIFUGE_KREPORT (krona_input.centrifuge, ch_input_for_centrifuge.db)
+    // ch_versions        = ch_versions.mix( /CENTRIFUGE_KREPORT.out.versions.first() )
+
+    emit:
+    versions       = ch_versions                 // channel: [ versions.yml ]
+}
+

subworkflows/local/profiling.nf

@@ -5,11 +5,7 @@
 include { MALT_RUN                                 } from '../../modules/nf-core/modules/malt/run/main'
 include { MEGAN_RMA2INFO                           } from '../../modules/nf-core/modules/megan/rma2info/main'
 include { KRAKEN2_KRAKEN2                          } from '../../modules/nf-core/modules/kraken2/kraken2/main'
-include { KRAKENTOOLS_KREPORT2KRONA                } from '../../modules/nf-core/modules/krakentools/kreport2krona/main'
-include { KRONA_CLEANUP as KRONA_KRAKENCLEANUP     } from '../../modules/local/krona_cleanup'
-include { KRONA_KTIMPORTTEXT as KRONA_IMPORTKRAKEN } from '../../modules/nf-core/modules/krona/ktimporttext/main'
 include { CENTRIFUGE_CENTRIFUGE                    } from '../../modules/nf-core/modules/centrifuge/centrifuge/main'
-include { CENTRIFUGE_KREPORT                       } from '../../modules/nf-core/modules/centrifuge/kreport/main'
 include { METAPHLAN3                               } from '../../modules/nf-core/modules/metaphlan3/main'
 include { KAIJU_KAIJU                              } from '../../modules/nf-core/modules/kaiju/kaiju/main'
 include { KAIJU_KAIJU2TABLE                        } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
@@ -25,7 +21,7 @@ workflow PROFILING {
     ch_versions             = Channel.empty()
     ch_multiqc_files        = Channel.empty()
     ch_raw_profiles         = Channel.empty()
-    ch_visualizations  = Channel.empty()
+    ch_output_for_krona     = Channel.empty()
 
 /*
         COMBINE READS WITH POSSIBLE DATABASES
@@ -128,16 +124,10 @@ workflow PROFILING {
                                 }
 
         KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db, params.kraken2_save_reads, params.kraken2_save_readclassification )
-        KRAKENTOOLS_KREPORT2KRONA ( KRAKEN2_KRAKEN2.out.report )
-        KRONA_KRAKENCLEANUP ( KRAKENTOOLS_KREPORT2KRONA.out.txt )
-        KRONA_IMPORTKRAKEN( KRONA_KRAKENCLEANUP.out.txt.map{[[id: it[0].db_name], it[1]]}.groupTuple() )
 
         ch_multiqc_files    = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report.collect{it[1]}.ifEmpty([])  )
-        ch_visualizations  = ch_visualizations.mix( KRONA_IMPORTKRAKEN.out.html )
+        ch_output_for_krona = ch_output_for_krona.mix( KRAKEN2_KRAKEN2.out.report )
         ch_versions         = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
-        ch_versions        = ch_versions.mix( KRAKENTOOLS_KREPORT2KRONA.out.versions.first() )
-        ch_versions        = ch_versions.mix( KRONA_KRAKENCLEANUP.out.versions.first() )
-        ch_versions        = ch_versions.mix( KRONA_IMPORTKRAKEN.out.versions.first() )
         ch_raw_profiles     = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report )
 
     }
@@ -156,9 +146,11 @@ workflow PROFILING {
                                 }
 
         CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_reads, params.centrifuge_save_reads, params.centrifuge_save_reads  )
-        CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.results, ch_input_for_centrifuge.db)
+        // TODO PUSH BACK CENTRIFUGE_KREPORT HERE WHERE DATABASE ALREADY IS?
+
+        ch_output_for_krona = ch_output_for_krona.mix( CENTRIFUGE_CENTRIFUGE.out.report )
         ch_versions         = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
-        ch_raw_profiles    = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
+        ch_raw_profiles     = ch_raw_profiles.mix( CENTRIFUGE_CENTRIFUGE.out.report )
 
     }
 
@@ -221,5 +213,5 @@ workflow PROFILING {
     profiles       = ch_raw_profiles    // channel: [ val(meta), [ reads ] ] - should be text files or biom
     versions       = ch_versions          // channel: [ versions.yml ]
     mqc            = ch_multiqc_files
-    visualizations = ch_visualizations
+    krona          = ch_output_for_krona
 }

workflows/taxprofiler.nf

@@ -62,6 +62,7 @@ include { SHORTREAD_HOSTREMOVAL         } from '../subworkflows/local/shortread_
 include { LONGREAD_HOSTREMOVAL          } from '../subworkflows/local/longread_hostremoval'
 include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
 include { PROFILING                     } from '../subworkflows/local/profiling'
+include { POSTPROCESSING_KRONA          } from '../subworkflows/local/postprocessing_krona'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -209,6 +210,13 @@ workflow TAXPROFILER {
     PROFILING ( ch_reads_runmerged, DB_CHECK.out.dbs )
     ch_versions = ch_versions.mix( PROFILING.out.versions )
 
+    /*
+        SUBWORKFLOW: KRONA VISUALISATION
+    */
+    POSTPROCESSING_KRONA ( PROFILING.out.krona, DB_CHECK.out.dbs )
+    ch_versions = ch_versions.mix( POSTPROCESSING_KRONA.out.versions )
+
+
     /*
         MODULE: MultiQC
     */