We produce monthly reports describing seasonal influenza circulation patterns. A substantial portion of time spent on these reports is tedious copying and pasting or running commands manually that could be automated.
Description
The following specific tasks will minimize the manual work associated with reports and allow us to focus on the science.
[x] Schedule nextflu-private builds to run and deploy after data upload (like the public builds). This should be easy to do now. We need to add rules that produce dated Auspice JSONs and deploy these JSONs to the desired group.
[ ] Automatically generate Markdown tables of new sequences per clade and clade coverage by titer references. The workflow logic to do this was added in #129, but we still need to add explicit dependencies for tabulate to our Docker and Conda environments.
[x] Summarize all new sequences per clade using Nextclade annotations from the full dataset instead of using subsampled data associated with representative or titers builds. Depends on the addition of an earlier step in the workflow that runs Nextclade on all data as mentioned in https://github.com/nextstrain/seasonal-flu/issues/144.
[x] #173
[ ] #163
[ ] Automatically add links for the latest builds to the nextflu-private group landing page after builds have been deployed.
Context
We produce monthly reports describing seasonal influenza circulation patterns. A substantial portion of time spent on these reports is tedious copying and pasting or running commands manually that could be automated.
Description
The following specific tasks will minimize the manual work associated with reports and allow us to focus on the science.