23 move the contents within the runner config to the input dir config

[yaseminbridges]

Deprecation of the --config parameter in favour of expecting a fixed and pre-configured config.yaml in the input directory. Apologies for the large PR, I think this was unavoidable but this will definitely be beneficial for running the plugin easily.

Summary of changes:

1. README.md --> updated the README instructions
2. config.yaml --> updated the template config structure that should be placed in the input directory
3. pyproject.toml --> removed pyserde dependency
4. poetry.lock --> updated the lock file to reflect changes in dependencies
5. config_parser.py --> removed this file as it was used for parsing a separate configuration file expected in the --config parameter
6. post_process.py --> implemented new ExomiserConfigurations class which is parsed from the tool_specific_configurations field in the input directory configuration file
7. tool_specific_configuration_options.py --> added additional variables required within the config.yaml for the run process
8. run.py --> removed methods and classes that dealt with the application.properties file - this is not needed as all configurations for the application.properties is dealt with in the prepare step. Implemented new ExomiserConfigurations class .
9. runner.py --> parse the config in the input directory
10. test_run.py --> removed these tests as removed the methods in run.py
11. test_write_application_properties.py --> added variables required within config