nf-core
GSR-DB
Description of feature
Dear Developers, Thank you for an amazing pipeline! I have one question and request.
The question is whether the different databases can be used in the taxonomy profiling step. We are planning to use an example NCBI database?
Request; is it possible you will add the GSR-DB (https://journals.asm.org/doi/10.1128/msystems.00950-23) to your pipeline? We are highly willing to try the one :)
I know I am asking for a lot. however, who is not asking is not getting :)
Cheers Dorota Julia Buczek
It's usually rather straight-forward to add a database, at least for the two DADA2 functions we use (assignTaxonomy and addSpecies). One adds information to the conf/ref_databases.config, and it's available. This includes adding a formatting script or using one of the existing ones. If you're willing to try this, please ask any questions at the #ampliseq channel of the nf-core Slack: https://nf-co.re/join/slack.
The first step would be to see if you can get the database to work via manual entry using the --dada_ref_tax_custom, --dada_ref_tax_custom_sp and --dada_assign_taxlevels parameters, see the documentation here: https://nf-co.re/ampliseq/2.11.0/parameters/#taxonomic-database and the documentation for the DADA2 functions: https://rdrr.io/bioc/dada2/man/assignTaxonomy.html and https://rdrr.io/bioc/dada2/man/addSpecies.html.
I close that as "not planned" for now, but please anyone re-open this in case someone wants to take action here.
