create log directories in Snakefile

• 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)

closes #70 (closed)

mentioned in commit c58f28df

merged