Skip to content

Add sbdi-gtdb=R10-RS226-1 and update sbdi-gtdb #879

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 4 commits into from
Apr 30, 2025
Merged

Add sbdi-gtdb=R10-RS226-1 and update sbdi-gtdb #879

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
ec60a7d
Add sbdi-gtdb=R10-RS226-1 and update sbdi-gtdb
erikrikarddaniel Apr 30, 2025
b812e70
Changelog
erikrikarddaniel Apr 30, 2025
d6cfea2
Move changelog entry
erikrikarddaniel Apr 30, 2025
7da22be
Move changelog entry to 2.14
erikrikarddaniel Apr 30, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,8 @@ 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`.

### `Changed`

- [#871](https://github.com/nf-core/ampliseq/pull/871) - Multi-region analysis is now easier with custom databases. No alignment file of the reference sequences are needed.
Expand Down
16 changes: 12 additions & 4 deletions conf/ref_databases.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -144,11 +144,19 @@ params {
dbversion = "RDP 18/11.5 (https://zenodo.org/records/4310151/)"
}
'sbdi-gtdb' {
title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R09-RS220-2"
file = [ "https://figshare.scilifelab.se/ndownloader/files/52432202", "https://figshare.scilifelab.se/ndownloader/files/52432214" ]
citation = "Lundin D, Andersson A. SBDI Sativa curated 16S GTDB database. FigShare. doi: 10.17044/scilifelab.14869077.v6"
title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R10-RS226-1"
file = [ "https://figshare.scilifelab.se/ndownloader/files/54036401", "https://figshare.scilifelab.se/ndownloader/files/54036416" ]
citation = "Lundin D, Andersson A. SBDI Sativa curated 16S GTDB database. FigShare. doi: 10.17044/scilifelab.14869077.v9"
fmtscript = "taxref_reformat_sbdi-gtdb.sh"
dbversion = "SBDI-GTDB-R09-RS220-2 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/8)"
dbversion = "SBDI-GTDB-R10-RS226-1 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/9)"
taxlevels = "Domain,Kingdom,Phylum,Class,Order,Family,Genus,Species"
}
'sbdi-gtdb=R10-RS226-1' {
title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R10-RS226-1"
file = [ "https://figshare.scilifelab.se/ndownloader/files/54036401", "https://figshare.scilifelab.se/ndownloader/files/54036416" ]
citation = "Lundin D, Andersson A. SBDI Sativa curated 16S GTDB database. FigShare. doi: 10.17044/scilifelab.14869077.v9"
fmtscript = "taxref_reformat_sbdi-gtdb.sh"
dbversion = "SBDI-GTDB-R10-RS226-1 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/9)"
taxlevels = "Domain,Kingdom,Phylum,Class,Order,Family,Genus,Species"
}
'sbdi-gtdb=R09-RS220-2' {
Expand Down
1 change: 1 addition & 0 deletions nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -429,6 +429,7 @@
"rdp",
"rdp=18",
"sbdi-gtdb",
"sbdi-gtdb=R10-RS226-1",
"sbdi-gtdb=R09-RS220-2",
"sbdi-gtdb=R09-RS220-1",
"sbdi-gtdb=R08-RS214-1",
Expand Down
2 changes: 1 addition & 1 deletion subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -234,7 +234,7 @@ def validateInputParameters() {
"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-RS220-2","sbdi-gtdb=R09-RS220-1", "sbdi-gtdb=R08-RS214-1","sbdi-gtdb=R07-RS207-1",
"sbdi-gtdb","sbdi-gtdb=R10-RS226-1","sbdi-gtdb=R09-RS220-2","sbdi-gtdb=R09-RS220-1", "sbdi-gtdb=R08-RS214-1","sbdi-gtdb=R07-RS207-1",
"silva","silva=138.2","silva=138","silva=132",
"unite-fungi","unite-fungi=10.0","unite-fungi=9.0","unite-fungi=8.3","unite-fungi=8.2",
"unite-alleuk","unite-alleuk=10.0","unite-alleuk=9.0","unite-alleuk=8.3","unite-alleuk=8.2"
Expand Down
Loading