From 9f0255b7cc5245c3eb0aa1c355ace2cba0f00438 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 27 Jul 2023 14:55:31 +0200 Subject: [PATCH] Update CHANGELOG --- CHANGELOG.md | 3 ++- subworkflows/local/profiling.nf | 6 +++++- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 748b0022..bb8e08e9 100644 --- a/CHANGELOG.md +++ b/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] diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf index dd7c844d..e6bbfc51 100644 --- a/subworkflows/local/profiling.nf +++ b/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 {