Update CHANGELOG

CHANGELOG.md

@@ -34,6 +34,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#313](https://github.com/nf-core/taxprofiler/pull/304) Fix pipeline not providing error when database sheet does not have a header (♥ to @noah472 for reporting, fix by @jfy133)
 - [#330](https://github.com/nf-core/taxprofiler/pull/330) Added better tagging to allow disambiguation of Kraken2 steps of Kraken2 vs Bracken (♥ to @MajoroMask for requesting, added by @jfy133)
 - [#334](https://github.com/nf-core/taxprofiler/pull/334) Increase the memory of the FALCO process to 4GB (fix by @LilyAnderssonLee)
+- [#338](https://github.com/nf-core/taxprofiler/pull/338) Fixed wrong file 'out' file going to `centrifuge kreport` module (♥ to @LilyAnderssonLee for reporting, fix by @jfy133)
 
 ### `Dependencies`
 
@@ -45,7 +46,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-- [#338](https://github.com/nf-core/taxprofiler/pull/338) Updated Centrifuge module to not generate (undocumented) SAM alignments by default if --save_centrifuge_reads supplied, to due Centrifuge bug modifying profile header. SAM alignments can still be generated if `--out-fmt` supplied in `database.csv` (♥ to @LilyAnderssonLee for reporting, fix by @jfy133)
+- [#338](https://github.com/nf-core/taxprofiler/pull/338) Updated Centrifuge module to not generate (undocumented) SAM alignments by default if --save_centrifuge_reads supplied, to due to a Centrifuge bug modifying profile header. SAM alignments can still be generated if `--out-fmt` supplied in `database.csv` (♥ to @LilyAnderssonLee for reporting, fix by @jfy133)
 
 ## v1.0.1 - Dodgy Dachshund Patch [2023-05-15]
 

subworkflows/local/profiling.nf

@@ -239,7 +239,11 @@ workflow PROFILING {
                                                 .filter { meta, db -> meta.tool == 'centrifuge' }
                                                 .map { meta, db -> [meta.db_name, meta, db] }
 
-        ch_input_for_centrifuge_kreport = CENTRIFUGE_CENTRIFUGE.out.report
+        // We must combine the _results_ file to get correct output - sending the report file will
+        // weirdly still produce valid-looking output, however the numbers are nonsense.
+        // Unfortunately the Centrifuge documentation for this was unclear as to _which_ outfile
+        // goes into it.
+        ch_input_for_centrifuge_kreport = CENTRIFUGE_CENTRIFUGE.out.results
                                             .map { meta, profile -> [meta.db_name, meta, profile] }
                                             .combine(ch_database_for_centrifugekreport, by: 0)
                                             .multiMap {