refactor db_Cleaning

[sangeetabhatia03]

db_cleaning on main is broken.
On rebase_sars_new, I have fixed it. However it is a bit of a tangled mess.

• There is plenty of duplicated code
• Things that only need to called once e.g. pathogen specific cleaning, are wrapped up in functions. These should be converted to scripts.

This task needs major refactoring otherwise it will be impossible to maintain.
I suggest each pathogen team set up pathogen specific cleaning task, and once we are all happy with the outputs, we refactor out the common bits again.
Please start from rebase_sars_new