Daniel Lundin

I'm getting the same error, when the number of libraries gets over a certain number (v. 1.2.9; I tried both a Conda package running in a Singularity container and a...

People are apparently sequencing whole rRNA operons, but most databases are limited to a single gene, or ITS, per sequence. To assign taxonomy, one would hence have to cut down...

I suppose we were thinking of something general, and this sounds specific to ITS. OTOH, better to have something that works for the only use case I'm aware of than...

I think it would be best to add a `taxlevels` entry in the `conf/ref_databases.config`; see e.g. the `midori2-co1` entry.

It can, AFAIK, be any kind of script but it will be executed by the current container, so the interpreter needs to be in that and findable by whatever you...

I agree with my namesake, and was perhaps leaning towards relying on one image that includes all, which means both python and bash, but also sed. Not working with singularity...

> Yes, the QIIME2 container seems to be broken for docker (which is used for GitHub tests, but it is fine with singularity that I use to test the pipeline...

I have some colleagues working on other algorithms with the intention of integrating them here. Your 3rd way may hence come without you doing anything.

A few other things to do: * Make sure we have at least one test case for the export for all taxonomy databases * SH to `scientific_name`, rank: "Unranked" *...

Also check the `event` and `asv-table` tabs in https://docs.google.com/spreadsheets/d/1E0I9Kph7xn0PXYna8EhV2l4NSf5kLTyN/edit?usp=sharing&ouid=104658483348595508395&rtpof=true&sd=true