Generally better error messages and error checking

[biodataganache]

Several aspects here can be improved:

1. More informative error messages - potentially output to log files (which currently aren't really used)
2. Basic input and folder checking prior to running snakemake. Once snakemake is rolling it doesn't make pretty output and error messages. We should be checking for basic requirements in terms of files, etc.
3. More error checking? I think it should be implemented for some kinds of reasonable things