Merge pull request #752 from d4straub/add-gtdb-RS220

add GTDB RS220

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#751](https://github.com/nf-core/ampliseq/pull/751) - Added version R08-RS214 of curated GTDB 16S taxonomy: `sbdi-gtdb=R08-RS214-1` or `sbdi-gtdb` as parameter to `--dada_ref_taxonomy`
+- [#752](https://github.com/nf-core/ampliseq/pull/752) - Added version R09-RS220 of GTDB 16S taxonomy: `gtdb=R09-RS220` or `gtdb` as parameter to `--dada_ref_taxonomy`
 
 ### `Changed`
 

bin/taxref_reformat_gtdb.sh

@@ -1,10 +1,15 @@
 #!/bin/sh
 
-# Reads the ar* and bac* SSU fasta files from GTDB (after first untarring)
+# Reads the ar* and bac* SSU fasta files from GTDB (after first untarring/unzipping)
 # and outputs two new fasta files, one suitable for DADA2's assignTaxonomy()
 # and addSpecies() functions.
 
-# Untar any tar file in the working directory
+# Unzip any .fna.gz file in the working directory - versions 220 and newer
+for f in *.fna.gz; do
+    gunzip -c $f > $(basename "$f" .gz)
+done
+
+# Untar any tar file in the working directory - versions 214.1 and older
 for f in *.tar.gz; do
     tar xzf $f
 done

conf/ref_databases.config

@@ -26,11 +26,18 @@ params {
             dbversion = "COIDB 221216 (https://doi.org/10.17044/scilifelab.20514192.v2)"
         }
         'gtdb' {
-            title = "GTDB - Genome Taxonomy Database - Release R08-RS214.1"
-            file = [ "https://data.ace.uq.edu.au/public/gtdb/data/releases/release214/214.1/genomic_files_reps/bac120_ssu_reps_r214.tar.gz", "https://data.ace.uq.edu.au/public/gtdb/data/releases/release214/214.1/genomic_files_reps/ar53_ssu_reps_r214.tar.gz" ]
+            title = "GTDB - Genome Taxonomy Database - Release R09-RS220"
+            file = [ "https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/genomic_files_reps/bac120_ssu_reps_r220.fna.gz", "https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/genomic_files_reps/ar53_ssu_reps_r220.fna.gz" ]
             citation = "Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, Hugenholtz P. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018 Nov;36(10):996-1004. doi: 10.1038/nbt.4229. Epub 2018 Aug 27. PMID: 30148503."
             fmtscript = "taxref_reformat_gtdb.sh"
-            dbversion = "GTDB R08-RS214.1 (https://data.ace.uq.edu.au/public/gtdb/data/releases/release214/214.1)"
+            dbversion = "GTDB R09-RS220 (https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0)"
+        }
+        'gtdb=R09-RS220' {
+            title = "GTDB - Genome Taxonomy Database - Release R09-RS220"
+            file = [ "https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/genomic_files_reps/bac120_ssu_reps_r220.fna.gz", "https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/genomic_files_reps/ar53_ssu_reps_r220.fna.gz" ]
+            citation = "Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, Hugenholtz P. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018 Nov;36(10):996-1004. doi: 10.1038/nbt.4229. Epub 2018 Aug 27. PMID: 30148503."
+            fmtscript = "taxref_reformat_gtdb.sh"
+            dbversion = "GTDB R09-RS220 (https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0)"
         }
         'gtdb=R08-RS214' {
             title = "GTDB - Genome Taxonomy Database - Release R08-RS214.1"

nextflow_schema.json

@@ -360,6 +360,7 @@
                         "gtdb=R06-RS202",
                         "gtdb=R07-RS207",
                         "gtdb=R08-RS214",
+                        "gtdb=R09-RS220",
                         "midori2-co1",
                         "midori2-co1=gb250",
                         "pr2",

subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf

@@ -237,7 +237,7 @@ 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=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=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)) ) {