The user should be able to decide if MIRFLOWZ is the correct tool for them to use by reading how it works in the documentation.

To achieve so extend the explanation in the main README.md to include details on:

• how the counting is done
• how the mapping and filtering are done
• the output files the user will get with some examples

In addition, in the pipeline_documentation.md, include examples of the common and edge cases that highlight the workflow behavior.