James A. Fellows Yates
James A. Fellows Yates
For the time being we've uploaded the mock db to github here: https://github.com/nf-core/test-datasets/tree/mag/databases/gtdbtk as our tests were really slow (download taking >1h in some cases) , but we are happy...
Oh that's very exciting, Thanks @pchaumeil !
Yes please! This will be come more common with nf-core now we have pipeline level tests too
Note this PR also includes a full 'specification' document that describe how each MIxS term _and_ the equivalent LinkML slot version of each term should 'look like'
I'm not up to date with the latest with BBTools, so I cannot really evaluate. But maybe first: @ewels what is your policy on deprecation in the MultiQC world?
Although now looking at your PR @fgvieira , I'm vaguely remembering that bbmap/tools had a different structure to bbduk or something like that, thus the extra nesting... It might not...
Potentially, let's see what @ewels says about module deprecation :)
> I made PR [#3398](https://github.com/MultiQC/MultiQC/pull/3398) (and [MultiQC/test-data#359](https://github.com/MultiQC/test-data/pull/359)) with some changes to the bbmap/bbtools module (e.g. fixing the json output and renaming the module). > > [@jfy133](https://github.com/jfy133) can you double check...
Note I would suggest putting in draft mode rather than 'DO NOT MERGE' in the title ;)
Are there dedicated LinkML attributes already for this? Or would this come under annotations or similar?