Skip to content
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

Remove phytoref #710

Merged
merged 6 commits into from
Mar 18, 2024
+2 −9
Merged

Remove phytoref #710

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
f3c97e1
Merge pull request #690 from nf-core/dev
d4straub Jan 15, 2024
256fc6b
removed phytoref
Mar 18, 2024
9f25806
CHANGELOG
Mar 18, 2024
5b5cd78
updated changelog
Mar 18, 2024
3f4a64e
removed phytoref from schema.json
Mar 18, 2024
daa9dce
Update CHANGELOG.md
danilodileo Mar 18, 2024
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 @@ -30,6 +30,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Removed`

- [#710](https://github.com/nf-core/ampliseq/pull/710) - Removed Phyloref from DADA2 reference option because it's part of PR2 5.0.0

## nf-core/ampliseq version 2.7.1 - 2023-11-14

### `Added`
Expand Down
8 changes: 0 additions & 8 deletions conf/ref_databases.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -76,14 +76,6 @@ params {
dbversion = "MIDORI2-CO1 GB250 (http://reference-midori.info/download/Databases/GenBank250/DADA2_sp/uniq/MIDORI2_UNIQ_NUC_SP_GB250_CO1_DADA2.fasta.gz)"
taxlevels = "Phylum,Class,Order,Family,Genus,Species"
}
'phytoref' {
title = "PhytoRef plastid 16S rRNA database for photosynthetic eukaryotes"
file = [ "http://phytoref.sb-roscoff.fr/static/downloads/PhytoRef_with_taxonomy.fasta" ]
citation = "Decelle, Johan, Sarah Romac, Rowena F. Stern, El Mahdi Bendif, Adriana Zingone, Stéphane Audic, Michael D. Guiry, et al. 2015. PhytoREF: A Reference Database of the Plastidial 16S rRNA Gene of Photosynthetic Eukaryotes with Curated Taxonomy. Molecular Ecology Resources 15 (6): 1435–45. https://doi.org/10.1111/1755-0998.12401."
fmtscript = "taxref_reformat_phytoref.sh"
dbversion = "unversioned"
taxlevels = "Domain,Supergroup,Subphylum,Class,Subclass,Order,Suborder,Family,Genus,Species"
}
'pr2' {
title = "PR2 - Protist Reference Ribosomal Database - Version 5.0.0"
file = [ "https://github.com/pr2database/pr2database/releases/download/v5.0.0/pr2_version_5.0.0_SSU_dada2.fasta.gz", "https://github.com/pr2database/pr2database/releases/download/v5.0.0/pr2_version_5.0.0_SSU_UTAX.fasta.gz" ]
Expand Down
1 change: 0 additions & 1 deletion nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -344,7 +344,6 @@
"gtdb=R08-RS214",
"midori2-co1",
"midori2-co1=gb250",
"phytoref",
"pr2",
"pr2=4.13.0",
"pr2=4.14.0",
Expand Down
Loading