Refactor LabKey to Snakemake script

- clean up command line interface
  - improve descriptions
  - add consistent structure
  - remove or merge superfluous CLI arguments
  - set defaults
  - update test calls
  - update docs
  - when importing data from LabKey, table is saved to 'samples.tsv.labkey' in same directory as Snakemake sample table
- allow user to specify environment variables and relative paths in input table and on CLI
  - relative paths in the input table are interpreted with respect to the directory containing the input table
  - relative paths will are interpreted with respect to the current working directory; this is to achieve portability with respect to tests but is discouraged in production because its behavior is not very predictable from the user's perspective; consequently a warning is thrown
- set STAR index size to read length - 1
- remove `gtf_filtered` and `tr_fasta_filtered` and update Snakefiles and test sample tables accordingly
- rename some MultiQC report-related parameters and update Snakefiles and test config files accordingly
- add logging
- add docstrings to module and all functions
- add typing definitions to all functions
- restructure and comment code to improve readability
- linters `flake8` and `mypy` pass