Create VISUALIZATION_KRONA workflow to create Krona charts

subworkflows/local/visualization_krona.nf

@@ -0,0 +1,55 @@
+//
+// Create Krona visualizations
+//
+
+include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/modules/krakentools/kreport2krona/main'
+include { KRONA_CLEANUP             } from '../../modules/local/krona_cleanup'
+include { KRONA_KTIMPORTTEXT        } from '../../modules/nf-core/modules/krona/ktimporttext/main'
+
+workflow VISUALIZATION_KRONA {
+    take:
+    profiles
+
+    main:
+    ch_krona_text = Channel.empty()
+    ch_krona_html = Channel.empty()
+    ch_versions = Channel.empty()
+
+    /*
+        Split profile results based on tool they come from
+    */
+    ch_input_profiles = profiles
+        .branch {
+            kraken2: it[0]['tool'] == 'kraken2'
+            unknown: true
+        }
+
+    /*
+        Convert Kraken2 formatted reports into Krona text files
+    */
+    ch_kraken_reports = ch_input_profiles.kraken2
+    KRAKENTOOLS_KREPORT2KRONA ( ch_kraken_reports )
+    ch_krona_text = ch_krona_text.mix( KRAKENTOOLS_KREPORT2KRONA.out.txt )
+    ch_versions = ch_versions.mix( KRAKENTOOLS_KREPORT2KRONA.out.versions.first() )
+
+    /*
+        Remove taxonomy level annotations from the Krona text files
+    */
+    KRONA_CLEANUP( ch_krona_text )
+    ch_cleaned_krona_text = KRONA_CLEANUP.out.txt
+    ch_versions = ch_versions.mix( KRONA_CLEANUP.out.versions.first() )
+
+    /*
+        Convert Krona text files into html Krona visualizations
+    */
+    ch_krona_text_for_import = ch_cleaned_krona_text
+        .map{[[id: it[0]['db_name']], it[1]]}
+        .groupTuple()
+    KRONA_KTIMPORTTEXT( ch_krona_text_for_import )
+    ch_krona_html = ch_krona_html.mix( KRONA_KTIMPORTTEXT.out.html )
+    ch_versions = ch_versions.mix( KRONA_KTIMPORTTEXT.out.versions.first() )
+
+    emit:
+    html = ch_krona_html
+    versions = ch_versions
+}