Description

Updated medaka version and dependencies. Update necessitated various changes regarding in- and output files and the required shell commands.

Related Issue

[x] I've formatted the PR title in accordance with the structure of the conventional commit messages.
[x] I've updated the code style using pre-commit if needed.
[x] I've updated or supplemented the documentation as needed.
[x] I've read the CODE_OF_CONDUCT.md document.
[x] I've read the CONTRIBUTING.md guide.