Matthias De Smet

Is that something you can make happen?

I'm not really sure this in the scope of a demultiplexing workflow. Sounds to me like that's more like extensive input QC to be done before starting a wf.

No problem, we can keep te issue around for the future Will there be room on the refgenie server for a kraken database?

Also, does kraken support remote db's or does it have to be local? e.g., can it read its files straight from S3 (for example) or does it have to stage...

I _think_ I made a point of naming the nf-core samplesheet as `flowcells.csv` to have a better distinction

Hi, Are you able to share your samplesheet(s) and your `.nextflow.log`? M

Perhaps we can just add a "demultiplexer" field to the input csv? Seems like the easiest way to go and it doesn't lock in the file name of the demultiplexer...

can be fixed by grabbing `out[4]` in stead of `out[2]` Cheers M

Seconded, same issue here

Why not ditch Flask and go full ASGI with automatic swagger/OpenAPI? I've been using [fastapi](https://fastapi.tiangolo.com) with huge success, and @tiangolo is a huge help when encountering issues. This would of...