Kevin Menden

Okay so we want to generate the `genomes.config` file automatically using refgenie. If I understand this correctly though, then we basically have to add all the assets to the refgenie...

Yup agree, and hopefully even the CI test won't be too difficult. Once all the assets are on the refgenie server, it _should_ be straightforward

Checking which assets currently available in iGenomes have corresponding recipes available in refgenie. https://github.com/refgenie/refgenie/blob/master/refgenie/asset_build_packages.py * [x] fasta * [x] bwa * [x] bowtie2 * [x] star * [x] bismark *...

I can't give you the exact list of dependencies right now, but those sound about right. I basically just collected all the dependencies that were necessary and combined their JARs....

Hi @sralchemab, I will try to have a look today and come back to you this evening, so for the delay!

Sorry - didn't geht around to check this week, but will do today :) will let you know

Alright, so unfortunately I don't have any notes about the exact versions used for putting together the JAR file anymore - definitely a bit of a mess up on my...

I have been out of the project for a bit so I can't tell you exactly where it used now. But the schema validation library is used to check whether...

Made a draft PR for `salmon alevin` here: https://github.com/nf-core/modules/pull/397 So I checked it off the list. Works locally with some test data but that's too big for uploading so I'm...

I just checked what is still missing, I think there is an open PR for `kallisto/quant` here: https://github.com/nf-core/modules/pull/351 So no need to do that again. Will have a look later...