Tests meta issue

[LevanBokeria]

Right now, the tests for synthetic and real parts of the pipeline are some developed using old expected input/output files and some using new ones since the code has evolved.

We should streamline them so they use the latest input/output files using the latest code and configurations.

[LevanBokeria]

One idea would be to just run the combined_pipeline.py with certain parameters for both real and synthetic data, and then have a dedicated location in the tests folder for those results, which will serve as both inputs and expected outputs for the different modules. So we won't need to have module-specific input folder and expected_outputs folders.