Integration test script path fix

[AngryMaciek]

Description

We cannot hard-code paths within the Snakefile like: python ../../../workflow/scripts/combine-motevo-results.py
I have fixed the problem with encoding the pipeline path into the config.yml file for snakemake (the user would have to provide it). Having this field we may encode in the Snakefile a relative path to the script from the cwd being the repository root directory.

The issue required some minor changes in the integration tests bash scripts - from now on snakemake is being executed from the repository root directory as well.

Type of change

• [x] Bug fix (non-breaking change which fixes an issue)
• [x] Breaking change (fix or feature that would cause existing functionality to not work as expected)

Checklist:

• [x] My code follows the style guidelines of this project
• [x] I have performed a self-review of my own code
• [x] I have commented my code, particularly in hard-to-understand areas
• [x] My changes generate no new warnings
• [x] I have added tests that prove my fix is effective or that my feature works
• [x] New and existing unit tests pass locally with my changes
• [x] I have not reduced the existing code coverage

[AngryMaciek]

All checks passed, this was a minor modification, I merge the branch now.
@krish8484 , take a look, just FYI.

[krish8484]

Okay, thanks @AngryMaciek !