Bugfix release

A bad bug was in version 2.2.1 (now 2.2.1-deprecated). This release fixes the bug and adds additional runtime checks to improve the workflows safety. Refactorings and documentation are also included.

2.2.1-deprecated: Merge pull request #1 from DKFZ-ODCF/fix-yet-another-bug-with-bad-data

Release was retracted. In rare cases it is possible that corrupt files are produced. Note that all cases we observed also resulted in failure of the annotation job. Retraction of the release is thus a safety-measure. If you still use this version, please check your output.