Site specific configurations

[pbiology]

How are we dealing with site specific configs? Should each site just keep their own configs outside of the repo, or should we have them in conf/gothenburg.config for instance?

I see a pro where new sites then have some material where they can copy others and use as a template. Also it's nice to have stuff in the same place as well.

Downsides I guess is that there will be a bunch of stuff not relevant for the pipeline.

[sylvinite]

There are two considerations:

• This repo is public. That means the site must be comfortable sharing their configs including file paths
• Every time a site wants to change their on site configuration, they have to modify genomic-medicine-sweden /
  gms-artic

I think the best course of action is to have a basic configuration here, and then a site specific override (if necessary) stored locally on site.

[pbiology]

OK. But then perhaps a structure for such a configuration file, and then site-specific config files stored outside the repo. I'm running a branch now to set up such a system so when done I can do a pull-request for this