Merge pull request #710 from danilodileo/remove-phytoref

Remove phytoref
nf-core · Mar 18, 2024 · e366469 · e366469
2 parents 2a23b1b + daa9dce
commit e366469
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -46,6 +46,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Removed`
 
+- [#710](https://github.com/nf-core/ampliseq/pull/710) - Removed Phyloref from DADA2 reference option because it's part of PR2 5.0.0
+
 ## nf-core/ampliseq version 2.7.1 - 2023-11-14
 
 ### `Added`

diff --git a/conf/ref_databases.config b/conf/ref_databases.config
@@ -76,14 +76,6 @@ params {
             dbversion = "MIDORI2-CO1 GB250 (http://reference-midori.info/download/Databases/GenBank250/DADA2_sp/uniq/MIDORI2_UNIQ_NUC_SP_GB250_CO1_DADA2.fasta.gz)"
             taxlevels = "Phylum,Class,Order,Family,Genus,Species"
         }
-        'phytoref' {
-            title = "PhytoRef plastid 16S rRNA database for photosynthetic eukaryotes"
-            file = [ "http://phytoref.sb-roscoff.fr/static/downloads/PhytoRef_with_taxonomy.fasta" ]
-            citation = "Decelle, Johan, Sarah Romac, Rowena F. Stern, El Mahdi Bendif, Adriana Zingone, Stéphane Audic, Michael D. Guiry, et al. 2015. PhytoREF: A Reference Database of the Plastidial 16S rRNA Gene of Photosynthetic Eukaryotes with Curated Taxonomy. Molecular Ecology Resources 15 (6): 1435–45. https://doi.org/10.1111/1755-0998.12401."
-            fmtscript = "taxref_reformat_phytoref.sh"
-            dbversion = "unversioned"
-            taxlevels = "Domain,Supergroup,Subphylum,Class,Subclass,Order,Suborder,Family,Genus,Species"
-        }
         'pr2' {
             title = "PR2 - Protist Reference Ribosomal Database - Version 5.0.0"
             file = [ "https://github.com/pr2database/pr2database/releases/download/v5.0.0/pr2_version_5.0.0_SSU_dada2.fasta.gz", "https://github.com/pr2database/pr2database/releases/download/v5.0.0/pr2_version_5.0.0_SSU_UTAX.fasta.gz" ]

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -349,7 +349,6 @@
                         "gtdb=R08-RS214",
                         "midori2-co1",
                         "midori2-co1=gb250",
-                        "phytoref",
                         "pr2",
                         "pr2=4.13.0",
                         "pr2=4.14.0",