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Co-authored-by: Moritz E. Beber <[email protected]>
nf-core · Oct 25, 2023 · da8bf5a · da8bf5a
1 parent bdd514d
commit da8bf5a
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Showing 3 changed files with 3 additions and 6 deletions.
diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
@@ -176,8 +176,8 @@ workflow PROFILING {
                 // Note may need to rename back to to just bracken in those downstream steps depending on context.
                 .map {
                     meta, report ->
-                        def new_tool = meta['tool'] == 'bracken' ? 'kraken2-bracken' : meta['tool']
-                    [meta + [tool: new_tool], report]
+                        def new_tool = 
+                    [meta + [tool: meta.tool == 'bracken' ? 'kraken2-bracken' : meta.tool], report]
                 }
         )
 

diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf
@@ -173,9 +173,7 @@ workflow STANDARDISATION_PROFILES {
                                         new_meta.db_name = meta.tool == 'kraken2-bracken' ? "${meta.db_name}-bracken" : "${meta.db_name}" // append so to disambiguate when we have same databases for kraken2 step of bracken, with normal bracken
                                     [ new_meta, profiles ]
                                 }
-                                .dump(tag: 'b4group')
                                 .groupTuple(sort: {-it.size()})
-                                .dump(tag: 'whatsgoingon')
 
     KRAKENTOOLS_COMBINEKREPORTS_KRAKEN ( ch_profiles_for_kraken2 )
     ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_KRAKEN.out.txt )

diff --git a/subworkflows/local/visualization_krona.nf b/subworkflows/local/visualization_krona.nf
@@ -43,8 +43,7 @@ workflow VISUALIZATION_KRONA {
     ch_kraken_reports = ch_input_profiles.kraken2
             .map {
                 meta, report ->
-                    def new_tool = meta['tool'] == 'kraken2-bracken' ? 'bracken' : meta['tool']
-                [meta + [tool: new_tool], report]
+                [meta +  [tool: meta.tool == 'bracken' ? 'kraken2-bracken' : meta.tool], report]
             }
             .mix( ch_input_profiles.centrifuge )
     KRAKENTOOLS_KREPORT2KRONA ( ch_kraken_reports )