outdated pydeseq2 argument 'clinical'

[e-coral]

Describe the bug
When running the capcruncher pipeline, I encounter 'TypeError: DeseqDataSet.init() got an unexpected keyword argument 'clinical''.

According to the pydeseq2 github page, 'clinical' was renamed 'metadata' a couple of years ago (scverse/PyDESeq2@f346162)

The capcruncher requirements file does not specify a version for pydeseq2, meaning that the latest version of pydeseq2 gets installed with fresh installations of capcruncher. Therefore, the 'clinical' argument is now invalid for the automatically installed version of pydeseq2.

To Reproduce
Steps to reproduce the behavior:
Install the most recent version of pydeseq2, and run capcruncher pipeline.

Expected behavior
Either:

1. specify a relevant older version of pydeseq2 in the requirements file
2. update def get_differential_interactions (interactions_differential.py) to use 'metadata' instead of 'clinical'
3. employ a version check and use the relevant argument for the version, similar to dds.deg_analysis function error omicverse/omicverse#163

[e-coral]

Changing 'clinical' to 'metadata' resolved this particular issue, but almost immediately led to other pydeseq2 argument issues, such as missing required arguments. Updating the tool to handle the new pydeseq2 API would be ideal, but seems to require significant work (I gave up after encountering 4 such successive errors).
Meanwhile, downgrading using pip install pydesqe2==0.3.5 has resolved pydeseq2 compatibility issues.

[alsmith151]

This should hopefully be fixed by #321