Merge pull request #879 from erikrikarddaniel/sbdi-gtdb-r226-1

Add sbdi-gtdb=R10-RS226-1 and update sbdi-gtdb

Author: erikrikarddaniel

CHANGELOG.md

@@ -7,6 +7,8 @@ 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`.
+
 ### `Changed`
 
 - [#871](https://github.com/nf-core/ampliseq/pull/871) - Multi-region analysis is now easier with custom databases. No alignment file of the reference sequences are needed.

conf/ref_databases.config

@@ -144,11 +144,19 @@ params {
             dbversion = "RDP 18/11.5 (https://zenodo.org/records/4310151/)"
         }
         'sbdi-gtdb' {
-            title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R09-RS220-2"
-            file = [ "https://figshare.scilifelab.se/ndownloader/files/52432202", "https://figshare.scilifelab.se/ndownloader/files/52432214" ]
-            citation = "Lundin D, Andersson A. SBDI Sativa curated 16S GTDB database. FigShare. doi: 10.17044/scilifelab.14869077.v6"
+            title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R10-RS226-1"
+            file = [ "https://figshare.scilifelab.se/ndownloader/files/54036401", "https://figshare.scilifelab.se/ndownloader/files/54036416" ]
+            citation = "Lundin D, Andersson A. SBDI Sativa curated 16S GTDB database. FigShare. doi: 10.17044/scilifelab.14869077.v9"
             fmtscript = "taxref_reformat_sbdi-gtdb.sh"
-            dbversion = "SBDI-GTDB-R09-RS220-2 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/8)"
+            dbversion = "SBDI-GTDB-R10-RS226-1 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/9)"
+            taxlevels = "Domain,Kingdom,Phylum,Class,Order,Family,Genus,Species"
+        }
+        'sbdi-gtdb=R10-RS226-1' {
+            title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R10-RS226-1"
+            file = [ "https://figshare.scilifelab.se/ndownloader/files/54036401", "https://figshare.scilifelab.se/ndownloader/files/54036416" ]
+            citation = "Lundin D, Andersson A. SBDI Sativa curated 16S GTDB database. FigShare. doi: 10.17044/scilifelab.14869077.v9"
+            fmtscript = "taxref_reformat_sbdi-gtdb.sh"
+            dbversion = "SBDI-GTDB-R10-RS226-1 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/9)"
             taxlevels = "Domain,Kingdom,Phylum,Class,Order,Family,Genus,Species"
         }
         'sbdi-gtdb=R09-RS220-2' {

nextflow_schema.json

@@ -429,6 +429,7 @@
                         "rdp",
                         "rdp=18",
                         "sbdi-gtdb",
+                        "sbdi-gtdb=R10-RS226-1",
                         "sbdi-gtdb=R09-RS220-2",
                         "sbdi-gtdb=R09-RS220-1",
                         "sbdi-gtdb=R08-RS214-1",

subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf

@@ -234,7 +234,7 @@ def validateInputParameters() {
         "midori2-co1","midori2-co1=gb250",
         "pr2","pr2=5.0.0","pr2=4.14.0","pr2=4.13.0",
         "rdp","rdp=18",
-        "sbdi-gtdb","sbdi-gtdb=R09-RS220-2","sbdi-gtdb=R09-RS220-1", "sbdi-gtdb=R08-RS214-1","sbdi-gtdb=R07-RS207-1",
+        "sbdi-gtdb","sbdi-gtdb=R10-RS226-1","sbdi-gtdb=R09-RS220-2","sbdi-gtdb=R09-RS220-1", "sbdi-gtdb=R08-RS214-1","sbdi-gtdb=R07-RS207-1",
         "silva","silva=138.2","silva=138","silva=132",
         "unite-fungi","unite-fungi=10.0","unite-fungi=9.0","unite-fungi=8.3","unite-fungi=8.2",
         "unite-alleuk","unite-alleuk=10.0","unite-alleuk=9.0","unite-alleuk=8.3","unite-alleuk=8.2"