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nf-core / ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2
https://nf-co.re/ampliseq
MIT License
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Adding gtdb release 214 & adding already downloaded database #636

Closed x-rv closed 1 year ago

x-rv commented 1 year ago

Description of feature

Hello!

GTDB has recently published a new release: https://data.gtdb.ecogenomic.org/releases/release214/ Could this be added to the supported databases?

Also, is it possible to indicate the path to an already downloaded database in the dada_ref_taxonomy option?

Thanks!

d4straub commented 1 year ago

GTDB has recently published a new release: https://data.gtdb.ecogenomic.org/releases/release214/ Could this be added to the supported databases?

Yes thats sounds important, thanks for the reminder!

Also, is it possible to indicate the path to an already downloaded database in the dada_ref_taxonomy option?

--dada_ref_tax_custom would allow that. But the databases are not so large and that shouldnt be a problem?! If you resume a run an already downloaded database will also be re-used and not downloaded again. Another option might be to use https://nf-co.re/docs/usage/offline (havent tried that myself).

d4straub commented 1 year ago

GTDB 214.1 is avaivale in the dev branch and will be in the next release!