- log and, if workflow is executed on cluster, cluster log directories are explicitly created in `Snakefile`
- location of main log directory can be configured in `config.yaml` (field `log_dir`, previously: `local_log`; requires change in script `labkey_to_snakemake.py` as well as subworkflows as field name is hard-coded there)
- location of cluster log directory can be configured in `cluster.json` (in field `__default__` -> `out`)
- `config.yaml` and `cluster.json` in `tests/input_files` are set such that a directory `logs/` is created in the directory where Snakemake is run (i.e., the directory of each test); cluster logs are stored in a subdirectory `logs/cluster`
- removes instructions to explicitly create log directories from docs and all test scripts
- cleans up main `Snakefile` (apart from Snakemake-specific syntax, now passes `flake8` linter test)