Merge pull request #786 from d4straub/fix-dada_ref_taxonomy-silva132

fix --dada_ref_taxonomy silva=132

Author: d4straub

CHANGELOG.md

@@ -7,13 +7,16 @@ 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`
 
 ### `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`
 

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"

nextflow_schema.json

@@ -479,6 +479,7 @@
                         "greengenes",
                         "greengenes=13.5",
                         "standard",
+                        "standard=20240904",
                         "standard=20230605"
                     ]
                 },