Add proper argument parsing in wgbs-pipeline.sh
Description of issue
A better way of input argument parsing should be implemented, including the MONITOR and SUBSET_READS options.
Options
-f/--force Force overwriting of results in existing folder -m/--monitor Monitor CPU and RAM --strategies Which strategies to carry (1,2,3,ALL) --continue-on-error If error is encountered in the pipeline, ignore and continue (unsets -e)