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May 2, 2025
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Add GTDB R10-RS226 #882

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Added`

- [#879](https://github.com/nf-core/ampliseq/pull/879) - Add `sbdi-gtdb=R10-RS226-1` as parameter to `--dada_ref_taxonomy` and make this version the default for `sbdi-gtdb`.
- [#882](https://github.com/nf-core/ampliseq/pull/882) - Add `gtdb=R10-RS226` as parameter to `--dada_ref_taxonomy` and make this version the default for `gtdb`.

### `Changed`

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13 changes: 10 additions & 3 deletions conf/ref_databases.config
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Expand Up @@ -40,11 +40,18 @@ params {
dbversion = "Greengenes2 2024.09 (https://zenodo.org/records/14169078)"
}
'gtdb' {
title = "GTDB - Genome Taxonomy Database - Release R09-RS220"
file = [ "https://data.gtdb.ecogenomic.org/releases/release220/220.0/genomic_files_reps/bac120_ssu_reps_r220.fna.gz", "https://data.gtdb.ecogenomic.org/releases/release220/220.0/genomic_files_reps/ar53_ssu_reps_r220.fna.gz" ]
title = "GTDB - Genome Taxonomy Database - Release R10-RS226"
file = [ "https://data.gtdb.ecogenomic.org/releases/release226/226.0/genomic_files_reps/bac120_ssu_reps_r226.fna.gz", "https://data.gtdb.ecogenomic.org/releases/release226/226.0/genomic_files_reps/ar53_ssu_reps_r226.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.gtdb.ecogenomic.org/releases/release220/220.0)"
dbversion = "GTDB R10-RS226 (https://data.gtdb.ecogenomic.org/releases/release226/226.0)"
}
'gtdb=R10-RS226' {
title = "GTDB - Genome Taxonomy Database - Release R10-RS226"
file = [ "https://data.gtdb.ecogenomic.org/releases/release226/226.0/genomic_files_reps/bac120_ssu_reps_r226.fna.gz", "https://data.gtdb.ecogenomic.org/releases/release226/226.0/genomic_files_reps/ar53_ssu_reps_r226.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 R10-RS226 (https://data.gtdb.ecogenomic.org/releases/release226/226.0)"
}
'gtdb=R09-RS220' {
title = "GTDB - Genome Taxonomy Database - Release R09-RS220"
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1 change: 1 addition & 0 deletions nextflow_schema.json
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Expand Up @@ -420,6 +420,7 @@
"gtdb=R07-RS207",
"gtdb=R08-RS214",
"gtdb=R09-RS220",
"gtdb=R10-RS226",
"midori2-co1",
"midori2-co1=gb250",
"pr2",
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2 changes: 1 addition & 1 deletion subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf
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Expand Up @@ -230,7 +230,7 @@ def validateInputParameters() {
String[] sbdi_compatible_databases = [
"coidb","coidb=221216",
"greengenes2","greengenes2=2024.09",
"gtdb","gtdb=R09-RS220","gtdb=R08-RS214","gtdb=R07-RS207","gtdb=R06-RS202","gtdb=R05-RS95",
"gtdb","gtdb=R10-RS226","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",
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