Create log directories in Snakefile

In response to #69 (closed), and due to the fact that the explicit creation of a cluster log directory is required for workflows to run at least on the Slurm cluster, log directories should be explicitly created at the start of the workflow file itself.

While at it, the layout of the log directories for the tests should be re-structured as well. Currently the following directories are generated:

• local_log
• logs/local_log => remains empty
• logs/cluster_log (only when executed with Slurm)

A structure with a single root log and a subdirectory for cluster files would be preferable.