Merge pull request #765 from erikrikarddaniel/sbdi-gtdb-r220

Add sbdi-gtdb R09-RS220
nf-core · Jul 23, 2024 · e66c9d3 · e66c9d3
2 parents 0fb5266 + 0b9a70b
commit e66c9d3
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Showing 4 changed files with 28 additions and 7 deletions.
diff --git 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`
 
+- [#765](https://github.com/nf-core/ampliseq/pull/765) - Added version R09-RS220 of curated GTDB 16S taxonomy: `sbdi-gtdb=R09-RS220-1` or `sbdi-gtdb` as parameter to `--dada_ref_taxonomy`
+
 ### `Changed`
 
 - [#762](https://github.com/nf-core/ampliseq/pull/762) - Improved output documentation section "Optional ASV filtering" and parameter documentation

diff --git a/conf/ref_databases.config b/conf/ref_databases.config
@@ -130,11 +130,19 @@ params {
             dbversion = "RDP 18/11.5 (https://zenodo.org/record/4310151/)"
         }
         'sbdi-gtdb' {
-            title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R08-RS214-1"
-            file = [ "https://figshare.scilifelab.se/ndownloader/files/45818841", "https://figshare.scilifelab.se/ndownloader/files/45818850" ]
+            title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R09-RS220-1"
+            file = [ "https://figshare.scilifelab.se/ndownloader/files/47244061", "https://figshare.scilifelab.se/ndownloader/files/47244076" ]
             citation = "Lundin D, Andersson A. SBDI Sativa curated 16S GTDB database. FigShare. doi: 10.17044/scilifelab.14869077.v6"
             fmtscript = "taxref_reformat_sbdi-gtdb.sh"
-            dbversion = "SBDI-GTDB-R08-RS214-1 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/6)"
+            dbversion = "SBDI-GTDB-R09-RS220-1 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/7)"
+            taxlevels = "Domain,Kingdom,Phylum,Class,Order,Family,Genus,Species"
+        }
+        'sbdi-gtdb=R09-RS220-1' {
+            title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R09-RS220-1"
+            file = [ "https://figshare.scilifelab.se/ndownloader/files/47244061", "https://figshare.scilifelab.se/ndownloader/files/47244076" ]
+            citation = "Lundin D, Andersson A. SBDI Sativa curated 16S GTDB database. FigShare. doi: 10.17044/scilifelab.14869077.v6"
+            fmtscript = "taxref_reformat_sbdi-gtdb.sh"
+            dbversion = "SBDI-GTDB-R09-RS220-1 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/7)"
             taxlevels = "Domain,Kingdom,Phylum,Class,Order,Family,Genus,Species"
         }
         'sbdi-gtdb=R08-RS214-1' {

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -372,10 +372,11 @@
                         "rdp",
                         "rdp=18",
                         "sbdi-gtdb",
-                        "sbdi-gtdb=R06-RS202-1",
-                        "sbdi-gtdb=R06-RS202-3",
-                        "sbdi-gtdb=R07-RS207-1",
+                        "sbdi-gtdb=R09-RS220-1",
                         "sbdi-gtdb=R08-RS214-1",
+                        "sbdi-gtdb=R07-RS207-1",
+                        "sbdi-gtdb=R06-RS202-3",
+                        "sbdi-gtdb=R06-RS202-1",
                         "silva",
                         "silva=132",
                         "silva=138",

diff --git a/subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf
@@ -237,7 +237,17 @@ def validateInputParameters() {
         error("Incompatible parameters: `--filter_ssu` cannot be used with `--skip_barrnap` because filtering for SSU's depends on barrnap.")
     }
 
-    String[] sbdi_compatible_databases = ["coidb","coidb=221216","gtdb","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","sbdi-gtdb","sbdi-gtdb=R08-RS214-1","sbdi-gtdb=R07-RS207-1","silva","silva=138","silva=132","unite-fungi","unite-fungi=9.0","unite-fungi=8.3","unite-fungi=8.2","unite-alleuk","unite-alleuk=9.0","unite-alleuk=8.3","unite-alleuk=8.2"]
+    String[] sbdi_compatible_databases = [
+        "coidb","coidb=221216",
+        "gtdb","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",
+        "sbdi-gtdb","sbdi-gtdb=R09-RS220-1","sbdi-gtdb=R08-RS214-1","sbdi-gtdb=R07-RS207-1",
+        "silva","silva=138","silva=132",
+        "unite-fungi","unite-fungi=9.0","unite-fungi=8.3","unite-fungi=8.2",
+        "unite-alleuk","unite-alleuk=9.0","unite-alleuk=8.3","unite-alleuk=8.2"
+    ]
     if (params.sbdiexport){
         if (params.sintax_ref_taxonomy ) {
             if (!Arrays.stream(sbdi_compatible_databases).anyMatch(entry -> params.sintax_ref_taxonomy.toString().equals(entry)) ) {