refactor: Allow mixing kaiju and kraken results

dalmolingroup · Mar 31, 2024 · 82059cf · 82059cf
1 parent 86952b5
commit 82059cf
Showing 1 changed file with 7 additions and 5 deletions.
diff --git a/subworkflows/local/taxonomy.nf b/subworkflows/local/taxonomy.nf
@@ -16,6 +16,8 @@ workflow TAXONOMY {
 
     main:
 
+    tax_report = Channel.empty()
+    krona_input = Channel.empty()
     ch_versions = Channel.empty()
 
     if (params.run_kaiju) {
@@ -35,10 +37,10 @@ workflow TAXONOMY {
             "species"
         )
 
-        KAIJU_KAIJU2TABLE.out.summary.set { tax_report }
+        tax_report = tax_report.mix(KAIJU_KAIJU2TABLE.out.summary)
 
         KAIJU_KAIJU2KRONA (kaiju_out, kaiju_db_files)
-        KAIJU_KAIJU2KRONA.out.txt.set { krona_input }
+        krona_input = krona_input.mix(KAIJU_KAIJU2KRONA.out.txt)
         ch_versions = ch_versions.mix(KAIJU_KAIJU2KRONA.out.versions)
     }
 
@@ -49,13 +51,13 @@ workflow TAXONOMY {
             false,
             false
         )
-        KRAKEN2_KRAKEN2.out.report.set { tax_report }
+        tax_report = tax_report.mix(KRAKEN2_KRAKEN2.out.report)
         ch_versions = ch_versions.mix(KRAKEN2_KRAKEN2.out.versions.first())
 
         KRAKENTOOLS_KREPORT2KRONA (
-            tax_report
+            KRAKEN2_KRAKEN2.out.report
         )
-        KRAKENTOOLS_KREPORT2KRONA.out.txt.set { krona_input }
+        krona_input = krona_input.mix(KRAKENTOOLS_KREPORT2KRONA.out.txt)
         ch_versions = ch_versions.mix(KRAKENTOOLS_KREPORT2KRONA.out.versions.first())
     }