Idea: wrap in workflow, running Nextclade and using that for substitution list

[corneliusroemer]

It might be nice to make a little workflow that first calls Nextclade, then use the private mutation output as the input for your tool. That way people don't need to curate a list..

[eringill]

I really like this idea! I've been investigating the CLI version of NextClade, but it seems that it requires the user to specify a reference, while the web application will generate suggestions for the best reference. How could I implement this functionality for the CLI? How does the web application do this on the fly?