design of chevron templates

[clarkliming]

in current snakemake POC approach, we are making the code structures clearer, filtering, reformating, run output, decoration, export.

In this structure, I am thinking of a question: shall we, expose the preprocessing, into the script?

In a lot of templates, preprocessing is required. However, it is not true that all these preprocessing is valid for all studies. I can expect changes needed for the preprocessing part, e.g. ae overview table, the variables needed can be very different in different studies, and using argument in run should not work because they are created in preprocessing. To allow user-defined preprocessing to be executed, the users need to change the template ( I don't think it is a good idea by the way). Another choice is that users can add preprocessing in the script

(I wonder if we should also expose the layout part in the script too. but it may affect the current "function argument based" "polymorphism", but we need to use some "variables" throughout the whole script.)