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Merge pull request #804 from jtangrot/update_unite10
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Update dada_ref_taxonomy with unite10
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@jtangrot
jtangrot authored Nov 21, 2024
2 parents 3f3cba5 + dd7a453 commit b350380
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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`

- [#804](https://github.com/nf-core/ampliseq/pull/804) - Added version 10 of Unite as parameter for `--dada_ref_taxonomy` (issue [#768](https://github.com/nf-core/ampliseq/issues/768))

### `Changed`

### `Fixed`
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36 changes: 26 additions & 10 deletions conf/ref_databases.config
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Expand Up @@ -199,12 +199,20 @@ params {
dbversion = "SILVA v132 (https://zenodo.org/record/1172783)"
}
'unite-fungi' {
title = "UNITE general FASTA release for Fungi - Version 9.0"
file = [ "https://s3.hpc.ut.ee/plutof-public/original/fa1038da-d18d-46b7-88a9-c21bcf38c43d.tgz" ]
citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2023): UNITE general FASTA release for Fungi. Version 18.07.2023. UNITE Community. https://doi.org/10.15156/BIO/2938067"
title = "UNITE general FASTA release for Fungi - Version 10.0"
file = [ "https://s3.hpc.ut.ee/plutof-public/original/d18aa648-3f4c-4f46-84d4-c8c5d48439ba.tgz" ]
citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE general FASTA release for Fungi. Version 04.04.2024. UNITE Community. https://doi.org/10.15156/BIO/2959332"
fmtscript = "taxref_reformat_unite.sh"
dbversion = "UNITE-fungi v9.0 (https://doi.org/10.15156/BIO/2938067)"
shfile = [ "https://figshare.scilifelab.se/ndownloader/files/50055762", "https://figshare.scilifelab.se/ndownloader/files/50055765"]
dbversion = "UNITE-fungi v10.0 (https://doi.org/10.15156/BIO/2959332)"
shfile = [ "https://figshare.scilifelab.se/ndownloader/files/50595459", "https://figshare.scilifelab.se/ndownloader/files/50595462"]
}
'unite-fungi=10.0' {
title = "UNITE general FASTA release for Fungi - Version 10.0"
file = [ "https://s3.hpc.ut.ee/plutof-public/original/d18aa648-3f4c-4f46-84d4-c8c5d48439ba.tgz" ]
citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE general FASTA release for Fungi. Version 04.04.2024. UNITE Community. https://doi.org/10.15156/BIO/2959332"
fmtscript = "taxref_reformat_unite.sh"
dbversion = "UNITE-fungi v10.0 (https://doi.org/10.15156/BIO/2959332)"
shfile = [ "https://figshare.scilifelab.se/ndownloader/files/50595459", "https://figshare.scilifelab.se/ndownloader/files/50595462"]
}
'unite-fungi=9.0' {
title = "UNITE general FASTA release for Fungi - Version 9.0"
Expand All @@ -231,12 +239,20 @@ params {
shfile = [ "https://scilifelab.figshare.com/ndownloader/files/34497971", "https://scilifelab.figshare.com/ndownloader/files/34497974"]
}
'unite-alleuk' {
title = "UNITE general FASTA release for eukaryotes - Version 9.0"
file = [ "https://s3.hpc.ut.ee/plutof-public/original/e318f5fd-1ef4-40fd-9e77-1b94d91b3858.tgz" ]
citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2023): UNITE general FASTA release for eukaryotes. Version 18.07.2023. UNITE Community. https://doi.org/10.15156/BIO/2938069"
title = "UNITE general FASTA release for eukaryotes - Version 10.0"
file = [ "https://s3.hpc.ut.ee/plutof-public/original/1dda2021-4893-4f2f-b50e-87bfea795267.tgz" ]
citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE general FASTA release for eukaryotes. Version 04.04.2024. UNITE Community. https://doi.org/10.15156/BIO/2959334"
fmtscript = "taxref_reformat_unite.sh"
dbversion = "UNITE-alleuk v9.0 (https://doi.org/10.15156/BIO/2938069)"
shfile = [ "https://figshare.scilifelab.se/ndownloader/files/50055768", "https://figshare.scilifelab.se/ndownloader/files/50055771"]
dbversion = "UNITE-alleuk v10.0 (https://doi.org/10.15156/BIO/2959334)"
shfile = [ "https://figshare.scilifelab.se/ndownloader/files/50595465", "https://figshare.scilifelab.se/ndownloader/files/50595471"]
}
'unite-alleuk=10.0' {
title = "UNITE general FASTA release for eukaryotes - Version 10.0"
file = [ "https://s3.hpc.ut.ee/plutof-public/original/1dda2021-4893-4f2f-b50e-87bfea795267.tgz" ]
citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE general FASTA release for eukaryotes. Version 04.04.2024. UNITE Community. https://doi.org/10.15156/BIO/2959334"
fmtscript = "taxref_reformat_unite.sh"
dbversion = "UNITE-alleuk v10.0 (https://doi.org/10.15156/BIO/2959334)"
shfile = [ "https://figshare.scilifelab.se/ndownloader/files/50595465", "https://figshare.scilifelab.se/ndownloader/files/50595471"]
}
'unite-alleuk=9.0' {
title = "UNITE general FASTA release for eukaryotes - Version 9.0"
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2 changes: 2 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -381,10 +381,12 @@
"silva=132",
"silva=138",
"unite-alleuk",
"unite-alleuk=10.0",
"unite-alleuk=9.0",
"unite-alleuk=8.3",
"unite-alleuk=8.2",
"unite-fungi",
"unite-fungi=10.0",
"unite-fungi=9.0",
"unite-fungi=8.3",
"unite-fungi=8.2",
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