Code review [ONGOING]

[venexia]

• Covariate file name. The wiki/Data-preparation#covariate-data says the static covariates file will be called pheno_covariates.txt but it is later referred to as static_covariates.txt.
• Simplify the numbering of steps. There is currently data preparation, setup, step 00, step 01, ... step 04. I think it would be more intuitive to number these as seven steps and make it clear whether data preparation should be done before or after setup.
• Provide a full variable list. It would have been helpful to have a full list of variables in one place, where an indicator for required/optional. I found myself reading through all the data preparation and making my own list of age, sex, BMI, etc. to perform the initial extract from the data.