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Add sbdi-gtdb R09-RS220 #765

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Jul 23, 2024
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Add sbdi-gtdb R09-RS220 #765

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2c4dc67
Add sbdi-gtdb R09-RS220
erikrikarddaniel Jul 23, 2024
0b9a70b
Updated CHANGELOG.md
erikrikarddaniel Jul 23, 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`

- [#765](https://github.com/nf-core/ampliseq/pull/765) - Added version R09-RS220 of curated GTDB 16S taxonomy: `sbdi-gtdb=R09-RS220-1` or `sbdi-gtdb` as parameter to `--dada_ref_taxonomy`

### `Changed`

- [#762](https://github.com/nf-core/ampliseq/pull/762) - Improved output documentation section "Optional ASV filtering" and parameter documentation
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14 changes: 11 additions & 3 deletions conf/ref_databases.config
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Expand Up @@ -130,11 +130,19 @@ params {
dbversion = "RDP 18/11.5 (https://zenodo.org/record/4310151/)"
}
'sbdi-gtdb' {
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" ]
title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R09-RS220-1"
file = [ "https://figshare.scilifelab.se/ndownloader/files/47244061", "https://figshare.scilifelab.se/ndownloader/files/47244076" ]
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)"
dbversion = "SBDI-GTDB-R09-RS220-1 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/7)"
taxlevels = "Domain,Kingdom,Phylum,Class,Order,Family,Genus,Species"
}
'sbdi-gtdb=R09-RS220-1' {
title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R09-RS220-1"
file = [ "https://figshare.scilifelab.se/ndownloader/files/47244061", "https://figshare.scilifelab.se/ndownloader/files/47244076" ]
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-R09-RS220-1 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/7)"
taxlevels = "Domain,Kingdom,Phylum,Class,Order,Family,Genus,Species"
}
'sbdi-gtdb=R08-RS214-1' {
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7 changes: 4 additions & 3 deletions nextflow_schema.json
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Expand Up @@ -372,10 +372,11 @@
"rdp",
"rdp=18",
"sbdi-gtdb",
"sbdi-gtdb=R06-RS202-1",
"sbdi-gtdb=R06-RS202-3",
"sbdi-gtdb=R07-RS207-1",
"sbdi-gtdb=R09-RS220-1",
"sbdi-gtdb=R08-RS214-1",
"sbdi-gtdb=R07-RS207-1",
"sbdi-gtdb=R06-RS202-3",
"sbdi-gtdb=R06-RS202-1",
"silva",
"silva=132",
"silva=138",
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12 changes: 11 additions & 1 deletion subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf
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Expand Up @@ -237,7 +237,17 @@ 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=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"]
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=R09-RS220-1","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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