Merge pull request #837 from chan-98/bugfix-refdb-zenodo

Changed path to RDP and SILVA ref files

Author: d4straub

CHANGELOG.md

@@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#837](https://github.com/nf-core/ampliseq/pull/837) - Replaced zenodo.org/record to zenodo.org/records in ref_databases.config
 - [#800](https://github.com/nf-core/ampliseq/pull/800) - Fixed SH files for UNITE9.0, they were missing some entries due to a bug caused by API update in PlutoF
 - [#808](https://github.com/nf-core/ampliseq/pull/808) - Add missing library declaration in R script.
 - [#832](https://github.com/nf-core/ampliseq/pull/832) - Add pattern to input field

conf/ref_databases.config

@@ -117,17 +117,17 @@ params {
         }
         'rdp' {
             title = "RDP - Ribosomal Database Project - RDP trainset 18/release 11.5"
-            file = [ "https://zenodo.org/record/4310151/files/rdp_train_set_18.fa.gz", "https://zenodo.org/record/4310151/files/rdp_species_assignment_18.fa.gz" ]
+            file = [ "https://zenodo.org/records/4310151/files/rdp_train_set_18.fa.gz", "https://zenodo.org/records/4310151/files/rdp_species_assignment_18.fa.gz" ]
             citation = "Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014 Jan;42(Database issue):D633-42. doi: 10.1093/nar/gkt1244. Epub 2013 Nov 27. PMID: 24288368; PMCID: PMC3965039."
             fmtscript = "taxref_reformat_standard.sh"
-            dbversion = "RDP 18/11.5 (https://zenodo.org/record/4310151/)"
+            dbversion = "RDP 18/11.5 (https://zenodo.org/records/4310151/)"
         }
         'rdp=18' {
             title = "RDP - Ribosomal Database Project - RDP trainset 18/release 11.5"
-            file = [ "https://zenodo.org/record/4310151/files/rdp_train_set_18.fa.gz", "https://zenodo.org/record/4310151/files/rdp_species_assignment_18.fa.gz" ]
+            file = [ "https://zenodo.org/records/4310151/files/rdp_train_set_18.fa.gz", "https://zenodo.org/records/4310151/files/rdp_species_assignment_18.fa.gz" ]
             citation = "Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014 Jan;42(Database issue):D633-42. doi: 10.1093/nar/gkt1244. Epub 2013 Nov 27. PMID: 24288368; PMCID: PMC3965039."
             fmtscript = "taxref_reformat_standard.sh"
-            dbversion = "RDP 18/11.5 (https://zenodo.org/record/4310151/)"
+            dbversion = "RDP 18/11.5 (https://zenodo.org/records/4310151/)"
         }
         'sbdi-gtdb' {
             title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R09-RS220-2"
@@ -201,17 +201,17 @@ params {
         }
         'silva=138' {
             title = "Silva 138.1 prokaryotic SSU"
-            file = [ "https://zenodo.org/record/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz", "https://zenodo.org/record/4587955/files/silva_species_assignment_v138.1.fa.gz" ]
+            file = [ "https://zenodo.org/records/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz", "https://zenodo.org/records/4587955/files/silva_species_assignment_v138.1.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"
-            dbversion = "SILVA v138.1 (https://zenodo.org/record/4587955)"
+            dbversion = "SILVA v138.1 (https://zenodo.org/records/4587955)"
         }
         'silva=132' {
             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" ]
+            file = [ "https://zenodo.org/records/1172783/files/silva_nr_v132_train_set.fa.gz", "https://zenodo.org/records/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"
-            dbversion = "SILVA v132 (https://zenodo.org/record/1172783)"
+            dbversion = "SILVA v132 (https://zenodo.org/records/1172783)"
         }
         'unite-fungi' {
             title = "UNITE general FASTA release for Fungi - Version 10.0"