diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
index 0d46e0c..5e2a7d2 100644
--- a/subworkflows/local/profiling.nf
+++ b/subworkflows/local/profiling.nf
@@ -41,7 +41,7 @@ workflow PROFILING {
             .combine(databases)
             .branch {
                 malt:    it[2]['tool'] == 'malt'
-                kraken2: it[2]['tool'] == 'kraken2'
+                kraken2: it[2]['tool'].contains('kraken2')
                 metaphlan3: it[2]['tool'] == 'metaphlan3'
                 centrifuge: it[2]['tool'] == 'centrifuge'
                 kaiju: it[2]['tool'] == 'kaiju'
@@ -131,34 +131,41 @@ workflow PROFILING {
         ch_multiqc_files       = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report )
         ch_versions            = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )
         ch_raw_classifications = ch_raw_classifications.mix( KRAKEN2_KRAKEN2.out.classified_reads_assignment )
-        ch_raw_profiles        = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report )
+        ch_raw_profiles        = ch_raw_profiles.mix(
+            KRAKEN2_KRAKEN2.out.report
+                // Set the tool to be strictly 'kraken2' instead of potentially 'kraken2+bracken' for downstream use.
+                .map { meta, report -> [meta + [tool: 'kraken2'], report]}
+        )
 
     }
 
     if ( params.run_kraken2 && params.run_bracken ) {
 
-        def ch_input_for_bracken
+        def ch_input_for_bracken = KRAKEN2_KRAKEN2.out.report
+            .filter { meta, report -> meta['tool'].contains('bracken') }
 
         if (params.kraken2_save_minimizers) {
-            ch_input_for_bracken = KRAKEN2_STANDARD_REPORT(KRAKEN2_KRAKEN2.out.report).report
-        } else {
-            ch_input_for_bracken = KRAKEN2_KRAKEN2.out.report
+            ch_input_for_bracken = KRAKEN2_STANDARD_REPORT(ch_input_for_bracken).report
         }
 
         ch_input_for_bracken = ch_input_for_bracken
             .combine(
                 databases.filter { meta, db ->
-                    meta['tool'] == 'bracken'
+                    meta['tool'].contains('bracken')
                 }
             )
             .multiMap { meta, report, db_meta, db ->
-                report: [meta + db_meta, report]
+                report: [meta, report]
                 db: db
             }
 
         BRACKEN_BRACKEN(ch_input_for_bracken.report, ch_input_for_bracken.db)
         ch_versions     = ch_versions.mix(BRACKEN_BRACKEN.out.versions.first())
-        ch_raw_profiles = ch_raw_profiles.mix(BRACKEN_BRACKEN.out.reports)
+        ch_raw_profiles = ch_raw_profiles.mix(
+            BRACKEN_BRACKEN.out.reports
+                // Set the tool to be strictly 'bracken' instead of potentially 'kraken2+bracken' for downstream use.
+                .map { meta, report -> [meta + [tool: 'bracken'], report]}
+        )
 
     }