Create a script to run the full pipeline to microreact

[tomersagi]

0. Find the latest result folder and update the config file
1. Run cleansing
2. Run to_mysql
3. run to_microreact

• [x] Clean up the scripts
• [x] Scripts should write to a log file.
• [x] Print out the log files when done.
• [x] Write files to ftp folder using a date naming system with a folder named latest for the latest files.
• [ ] Attach to nextstrain script (Rasmus)
• [x] Use replace uuid withgisaid_id`
• [x] Generate website data files
• [x] Send website data to the server
• [x] Change NUTS3 to NUTS2
• [ ] Setup sftp for microreact
• [ ] Change config with an authorized user