feat: irods download refactoring and new generic sodar downloader with preset for dragen data (#226 )

[Nicolai-vKuegelgen]

Fixes #226
Replaces #208

Partially fixes #201

[github-actions]

Please format your code with black: make black.

[codecov]

Codecov Report

Attention: Patch coverage is 77.73973% with 65 lines in your changes are missing coverage. Please review.

Project coverage is 81.50%. Comparing base (0f7f5b2) to head (cbf69e3).

❗ Current head cbf69e3 differs from pull request most recent head 447c235. Consider uploading reports for the commit 447c235 to get more accurate results

Files	Patch %	Lines
cubi_tk/sodar/pull_data_collection.py	70.07%	38 Missing ⚠️
cubi_tk/irods_common.py	70.00%	15 Missing ⚠️
cubi_tk/irods/check.py	42.85%	4 Missing ⚠️
cubi_tk/snappy/pull_data_common.py	80.00%	2 Missing ⚠️
cubi_tk/snappy/check_remote.py	50.00%	1 Missing ⚠️
cubi_tk/snappy/pull_processed_data.py	50.00%	1 Missing ⚠️
cubi_tk/snappy/pull_raw_data.py	50.00%	1 Missing ⚠️
cubi_tk/sodar/check_remote.py	50.00%	1 Missing ⚠️
cubi_tk/sodar_common.py	85.71%	1 Missing ⚠️
tests/test_sodar_pull_data_collection.py	98.38%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #227      +/-   ##
==========================================
+ Coverage   81.05%   81.50%   +0.45%     
==========================================
  Files         106      108       +2     
  Lines        8212     8380     +168     
==========================================
+ Hits         6656     6830     +174     
+ Misses       1556     1550       -6     

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[xiamaz]

Some comments from my side

[xiamaz]

lgtm

[tedil]

I can't really comment on the logic here, as I am not particularly familiar with irods, so most of my comments are small-ish and optional suggestions (regarding type hints and generators instead of list comprehensions).
I didn't mark all type hints, but with python 3.10+ (which I think is the minimum requirement for cubi-tk), you can simply use the builtin directly, no need to import from typing for most of them.