Consolidate collectstats into a single rule
The implementation is a bit hacky, since snakemake does not allow for optional input files. As a workaround, "." is passed when the bedfile is not defined, and the collect_stats.py script has been made aware of the special meaning of "." Additionally, Click has been removed as a dependency for collect stats, and the structure of the stats.json file has been updated to only allow for a single entry of coverage stats instead of a list. This has been done to match an earlier change in Hutspot where support for multiple bed files has been dropped.