Erin dev

[erinyoung]

This is intended to address :

• https://github.com/UPHL-BioNGS/Cecret/issues/67
• https://github.com/UPHL-BioNGS/Cecret/issues/81
• https://github.com/UPHL-BioNGS/Cecret/issues/89

[erinyoung]

Just running some tests.

Currently needing :

• update readme
• update config template
• update example files

[erinyoung]

Alright. Updated the config file and readme, and now just waiting on the tests.

[erinyoung]

The primer files aren't being read in correctly. Adjusting them and trying again.

[erinyoung]

All tests passed