Merge pull request #882 from d4straub/add-gtdb10-RS226

Add GTDB R10-RS226

Author: d4straub

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#879](https://github.com/nf-core/ampliseq/pull/879) - Add `sbdi-gtdb=R10-RS226-1` as parameter to `--dada_ref_taxonomy` and make this version the default for `sbdi-gtdb`.
+- [#882](https://github.com/nf-core/ampliseq/pull/882) - Add `gtdb=R10-RS226` as parameter to `--dada_ref_taxonomy` and make this version the default for `gtdb`.
 
 ### `Changed`
 

conf/ref_databases.config

@@ -40,11 +40,18 @@ params {
             dbversion = "Greengenes2 2024.09 (https://zenodo.org/records/14169078)"
         }
         'gtdb' {
-            title = "GTDB - Genome Taxonomy Database - Release R09-RS220"
-            file = [ "https://data.gtdb.ecogenomic.org/releases/release220/220.0/genomic_files_reps/bac120_ssu_reps_r220.fna.gz", "https://data.gtdb.ecogenomic.org/releases/release220/220.0/genomic_files_reps/ar53_ssu_reps_r220.fna.gz" ]
+            title = "GTDB - Genome Taxonomy Database - Release R10-RS226"
+            file = [ "https://data.gtdb.ecogenomic.org/releases/release226/226.0/genomic_files_reps/bac120_ssu_reps_r226.fna.gz", "https://data.gtdb.ecogenomic.org/releases/release226/226.0/genomic_files_reps/ar53_ssu_reps_r226.fna.gz" ]
             citation = "Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, Hugenholtz P. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018 Nov;36(10):996-1004. doi: 10.1038/nbt.4229. Epub 2018 Aug 27. PMID: 30148503."
             fmtscript = "taxref_reformat_gtdb.sh"
-            dbversion = "GTDB R09-RS220 (https://data.gtdb.ecogenomic.org/releases/release220/220.0)"
+            dbversion = "GTDB R10-RS226 (https://data.gtdb.ecogenomic.org/releases/release226/226.0)"
+        }
+        'gtdb=R10-RS226' {
+            title = "GTDB - Genome Taxonomy Database - Release R10-RS226"
+            file = [ "https://data.gtdb.ecogenomic.org/releases/release226/226.0/genomic_files_reps/bac120_ssu_reps_r226.fna.gz", "https://data.gtdb.ecogenomic.org/releases/release226/226.0/genomic_files_reps/ar53_ssu_reps_r226.fna.gz" ]
+            citation = "Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, Hugenholtz P. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018 Nov;36(10):996-1004. doi: 10.1038/nbt.4229. Epub 2018 Aug 27. PMID: 30148503."
+            fmtscript = "taxref_reformat_gtdb.sh"
+            dbversion = "GTDB R10-RS226 (https://data.gtdb.ecogenomic.org/releases/release226/226.0)"
         }
         'gtdb=R09-RS220' {
             title = "GTDB - Genome Taxonomy Database - Release R09-RS220"

nextflow_schema.json

@@ -420,6 +420,7 @@
                         "gtdb=R07-RS207",
                         "gtdb=R08-RS214",
                         "gtdb=R09-RS220",
+                        "gtdb=R10-RS226",
                         "midori2-co1",
                         "midori2-co1=gb250",
                         "pr2",

subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf

@@ -230,7 +230,7 @@ def validateInputParameters() {
     String[] sbdi_compatible_databases = [
         "coidb","coidb=221216",
         "greengenes2","greengenes2=2024.09",
-        "gtdb","gtdb=R09-RS220","gtdb=R08-RS214","gtdb=R07-RS207","gtdb=R06-RS202","gtdb=R05-RS95",
+        "gtdb","gtdb=R10-RS226","gtdb=R09-RS220","gtdb=R08-RS214","gtdb=R07-RS207","gtdb=R06-RS202","gtdb=R05-RS95",
         "midori2-co1","midori2-co1=gb250",
         "pr2","pr2=5.0.0","pr2=4.14.0","pr2=4.13.0",
         "rdp","rdp=18",