Add no_header to MethRatio from MethRatioWorkflow
Clean up shellcmd call
Stylistic changes
Include version check from MethRatioWorkflow
Attempt to rework output_dir/output_file

Keep the ability to set the output_file but also use the output_dir so
it matches the MethRatioWorkflow interface.
Remove MethRatioWorkflow
Cleanup reference logic