Add new subrelease of sbdi-gtdb: RS220-2

nf-core · Feb 18, 2025 · 559aba4 · 559aba4
1 parent e5e627d
commit 559aba4
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Showing 4 changed files with 13 additions and 3 deletions.
diff --git a/.gitignore b/.gitignore
@@ -7,3 +7,4 @@ testing/
 testing*
 *.pyc
 null/
+.nf-test*
diff --git a/conf/ref_databases.config b/conf/ref_databases.config
@@ -130,8 +130,16 @@ params {
             dbversion = "RDP 18/11.5 (https://zenodo.org/record/4310151/)"
         }
         'sbdi-gtdb' {
-            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" ]
+            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"
+            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=R09-RS220-2' {
+            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"
             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)"

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -416,6 +416,7 @@
                         "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",

diff --git a/subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf
@@ -232,7 +232,7 @@ 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-RS220-1","sbdi-gtdb=R08-RS214-1","sbdi-gtdb=R07-RS207-1",
+        "sbdi-gtdb","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"
-Original file line number
+Diff line change
@@ Expand Up / @@ -7,3 +7,4 @@ testing/ @@
     testing*
     *.pyc
     null/
+    .nf-test*