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Hey guys!
This is my attempt at implementing the updating of the small variant vcf list. I have used the code we run at HUS, which is reflected in this nextflow process, as a base.
I have defined classes for the vcf list and the different vcf files to be able to write methods and gather all input values in one place. Also I wanted to create a clean interface towards the cli. Logging is handled by the logger defined in the cli module. Testing is done with table-driven tests, meaning we have different test cases for each function and collect them in a list of objects which we loop over. This makes things DRYer and provides a better overview of what is tested.
Please ask and comment so we can figure out if this is a good way to handle things☺️