This combines #165 with the logging changes + #175 the 3.7.0 upgrade. The standalone upgrade to 3.7.0 didn't work, because it needs the logging changes
Note that there is a failing test, but it is already failing in master. We should address those in a separate PR. I'm guessing they are actually server issues since we get a status of annotation failed in the MAF
This combines #165 with the logging changes + #175 the 3.7.0 upgrade. The standalone upgrade to 3.7.0 didn't work, because it needs the logging changes
The description of https://github.com/genome-nexus/genome-nexus-annotation-pipeline/pull/165 is better, so please see the discussion there for a better explanation of the changes
Note that there is a failing test, but it is already failing in master. We should address those in a separate PR. I'm guessing they are actually server issues since we get a status of annotation failed in the MAF
This supersedes #165 and #175