Download improvements and more

This release addresses key issues with database files:

• The inbuilt domain for the eggNOG database has disappeared. The download tool now bypasses that to retrieve files from an alternative source.
• Both the eggNOG and KofamScan databases previously had problems so that previously downloaded files were not recognized because of the lack of a versions.yml file. This should now be fixed.

A number of other smaller bug fixes and additions are included, plus an upgrade to the latest nf-core template and modules.