Fix/non zero exitcode rsync

[ellendejong]

What has changed?

If rsync command failed, exitcode would stay 0.
Changed the implementation to check on returncode. Therefore replaced os.system with subprocess_run.

The non-zero returncode of rsync should result in a non-zero returncode of the script, by using sys.exit(). Moved the compress, index and rsync for exon measurements after the transcript measurements, so that these are still added to ExonCov.

Additional information

This is a bugfix. Therefore several items are ignored:

• Script doesnot pass flake8 and our coding style guides.
• Docstrings and unit tests not added.