Adds extensive testing and fixes from backlog

[mcamarad]

Summary:

Addresses fixes and improvements from gel-gwas backlog.

Tasks:

• [x] plinkTestCh is not used as input anywhere
• [x] Add tests to cover all run scenaria.
• [x] Fix null behaviour on report when LDSC is not executed
• [x] Refactor to have only one process
• [x] Opportunity for refactor: Flatten nested if (if (case_group != 'None'){
• [x] Opportunity for refactor: flatten nested ifs
• [x] Add exception in continuous data transformations to not be computed on PCs
• [x] Adds testing scenario for working with real pheno data and synthetic genotypes

Comments:

all_contrasts and case_vs_group_contrasts require high memory so it makes difficult CI tests. Removed from CI tests until the problem is addressed specifically. Card opened: https://github.com/lifebit-ai/gel-gwas/issues/71

Test in CloudOS

https://cloudos.lifebit.ai/app/jobs/5f9ace9a61aba101120efbe3

[mcamarad]

Thanks @cgpu !! Merging now and putting this in quarantine until tests and future fixes are done ✅