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sbdi-gtdb=R08-RS214-1 (r214) #751

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Jun 18, 2024
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sbdi-gtdb=R08-RS214-1 (r214) #751

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fe788f1
Added sbdi-gtdb=R08-RS214-1
erikrikarddaniel Jun 17, 2024
09207bf
CHANGELOG.md
erikrikarddaniel Jun 17, 2024
92f7fda
Update sbdi-gtdb to point to the latest
erikrikarddaniel Jun 18, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,8 @@ 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`

### `Changed`

### `Fixed`
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8 changes: 8 additions & 0 deletions conf/ref_databases.config
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Expand Up @@ -130,6 +130,14 @@ params {
dbversion = "SBDI-GTDB-R07-RS207-1 (https://scilifelab.figshare.com/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/4)"
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Key 'sbdi-gtdb' still leads to Release R07-RS207-1, wouldnt it be good to update it?

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Good catch! I've pushed an update.

taxlevels = "Domain,Kingdom,Phylum,Class,Order,Family,Genus,Species"
}
'sbdi-gtdb=R08-RS214-1' {
title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R08-RS214-1"
file = [ "https://figshare.scilifelab.se/ndownloader/files/45818841", "https://figshare.scilifelab.se/ndownloader/files/45818850" ]
citation = "Lundin D, Andersson A. SBDI Sativa curated 16S GTDB database. FigShare. doi: 10.17044/scilifelab.14869077.v6"
fmtscript = "taxref_reformat_sbdi-gtdb.sh"
dbversion = "SBDI-GTDB-R08-RS214-1 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/6)"
taxlevels = "Domain,Kingdom,Phylum,Class,Order,Family,Genus,Species"
}
'sbdi-gtdb=R07-RS207-1' {
title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R07-RS207-1"
file = [ "https://scilifelab.figshare.com/ndownloader/files/36980767", "https://scilifelab.figshare.com/ndownloader/files/36980788" ]
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1 change: 1 addition & 0 deletions nextflow_schema.json
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Expand Up @@ -372,6 +372,7 @@
"sbdi-gtdb=R06-RS202-1",
"sbdi-gtdb=R06-RS202-3",
"sbdi-gtdb=R07-RS207-1",
"sbdi-gtdb=R08-RS214-1",
"silva",
"silva=132",
"silva=138",
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2 changes: 1 addition & 1 deletion subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf
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Expand Up @@ -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=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=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)) ) {
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