Consider building templates for pipelines explicitly using pipeline software

[papsti]

Currently, episoap is geared toward easily generating template RMarkdown reports, which is great for analysts that don't want to get into code. However, analysts that are happy to get into code could also benefit from a template for common analysis upon which to build. One option would be to just output a template .R script, but scripts are often not very scalable as analyses get more complicated. Instead, you could consider outputting files that are compatible with pipeline software, like targets or orderly2.

I'm not sure if this is really within the scope of episoap but in general, it feels like the epiverse has a ton of very useful pieces for epi analyses that would benefit from being brought together in templates that could easily be called and built upon.

[Bisaloo]

Thanks a lot for your feedback! It is very valuable and timely, as we are currently rethinking our internal infrastructure for pipelines.

Integrating with targets and orderly2 has been on the roadmap from the start (#13, #14) but we've been unsure how much it should be prioritized, and how to do it in a way that is transparent for users unfamiliar with these tools.

I will bump this on the priority list for our roadmap and additional thoughts on this topic are very welcome ☺️