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
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
Describe alternatives you've considered NA / status quo
Additional context NA