Write initial integration test

Continuous integration was set up for this project in !5 (merged). However, currently there is only a very basic test (snakemake -n) set up. A test case should be carefully designed to verify that the pipeline works as expected. The necessary commands to execute these tests should then be added to the CI/CD configuration file .gitlab-ci.yml, in order to ensure that erroneous commits are not merged into the main code in the future.

Note that all test-related data, configuration and script files should be placed inside the tests directory or a sub-directory thereof.

Also note that no test may exceed the resource limits of the VM we are using for testing (4 cores, 8 Gb RAM, ~90 Gb disk space).

The command to run the test should be added to the documentation.