Add PhytoRef taxonomy database for chloroplast 16S

nf-core · Dec 11, 2023 · f61d945 · f61d945
1 parent fac3d73
commit f61d945
Show file tree

Hide file tree

Showing 3 changed files with 16 additions and 0 deletions.
diff --git a/bin/taxref_reformat_phytoref.sh b/bin/taxref_reformat_phytoref.sh
@@ -0,0 +1,7 @@
+#!/bin/sh
+
+# Write the assignTaxonomy() fasta file: assignTaxonomy.fna
+cat PhytoRef_with_taxonomy.fasta | sed '/>/s/>[^|]*|/>/' | sed '/>/s/|/;/g' > assignTaxonomy.fna
+
+# Write the addSpecies() fasta file: addSpecies.fna
+cat PhytoRef_with_taxonomy.fasta | sed '/^>/s/>\([^|]\+\)|.*|\([^|]\+\)/>\1 \2/' > addSpecies.fna
diff --git a/conf/ref_databases.config b/conf/ref_databases.config
@@ -76,6 +76,14 @@ 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 = "unknown"
+            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
@@ -344,6 +344,7 @@
                         "gtdb=R08-RS214",
                         "midori2-co1",
                         "midori2-co1=gb250",
+                        "phytoref",
                         "pr2",
                         "pr2=4.13.0",
                         "pr2=4.14.0",