Switch from icommand usage to the python irods client

[Nicolai-vKuegelgen]

Is your feature request related to a problem? Please describe.
Currently most cubi-tk functions that pull or push data to or from irods/Sodar rely on icommands that are accessed via subprocess and must be available in the current environment. These commands are not part of the stated (or easily/automatically installable) requirements for cubi-tk. The python irods client (which is already used by cubi-tk for other features) also allows transfer of files natively without the need to rely on 'external' dependencies and should be used instead.

Describe the solution you'd like

• Implementation of base classes &/ functions that allow file transfer with the native irods client
• change all current references to icommands to use these functions instead

Describe alternatives you've considered
NA / status quo

Additional context
NA