From 12c037095689f824d606624f50d54043c77f34d7 Mon Sep 17 00:00:00 2001 From: d4straub Date: Thu, 24 Oct 2024 10:34:43 +0200 Subject: [PATCH] fix --dada_ref_taxonomy silva=132 --- CHANGELOG.md | 3 +++ conf/ref_databases.config | 13 ++++++++++--- nextflow_schema.json | 1 + 3 files changed, 14 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 011fae01..1f6a8f26 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` +- [#786](https://github.com/nf-core/ampliseq/pull/786) - Added version 20240904 of Kraken2 standard taxonomy database: `standard=20240904` or `standard` as parameter to `--kraken2_ref_taxonomy` + ### `Changed` - [#785](https://github.com/nf-core/ampliseq/pull/785) - replaced https://data.ace.uq.edu.au/public/gtdb/data by https://data.gtdb.ecogenomic.org for GTDB versions via `--dada_ref_taxonomy` @@ -14,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` - [#785](https://github.com/nf-core/ampliseq/pull/785) - Template update for nf-core/tools version 3.0.2 +- [#786](https://github.com/nf-core/ampliseq/pull/786) - Creation of the summary report was failing with `--dada_ref_taxonomy silva=132` ### `Dependencies` diff --git a/conf/ref_databases.config b/conf/ref_databases.config index a87794fa..e640179a 100644 --- a/conf/ref_databases.config +++ b/conf/ref_databases.config @@ -192,7 +192,7 @@ params { dbversion = "SILVA v138.1 (https://zenodo.org/record/4587955)" } 'silva=132' { - title = "Silva Project's version 132 release" + title = "Silva Projects version 132 release" file = [ "https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz", "https://zenodo.org/record/1172783/files/silva_species_assignment_v132.fa.gz" ] citation = "Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6. doi: 10.1093/nar/gks1219. Epub 2012 Nov 28. PMID: 23193283; PMCID: PMC3531112." fmtscript = "taxref_reformat_standard.sh" @@ -528,8 +528,15 @@ params { taxlevels = "D,P,C,O,F,G,S" } 'standard' { - title = "Standard database - Version 20230605" - file = [ "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20230605.tar.gz" ] + title = "Standard database - Version 20240904" + file = [ "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20240904.tar.gz" ] + citation = "Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome biology, 20(1), 257. https://doi.org/10.1186/s13059-019-1891-0" + fmtscript = "" + taxlevels = "D,P,C,O,F,G,S" + } + 'standard=20240904' { + title = "Standard database - Version 20240904" + file = [ "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20240904.tar.gz" ] citation = "Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome biology, 20(1), 257. https://doi.org/10.1186/s13059-019-1891-0" fmtscript = "" taxlevels = "D,P,C,O,F,G,S" diff --git a/nextflow_schema.json b/nextflow_schema.json index 8ceba7b9..e0b263b2 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -479,6 +479,7 @@ "greengenes", "greengenes=13.5", "standard", + "standard=20240904", "standard=20230605" ] },