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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.
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 Make Markdown output for reports #129, but we still need to add explicit dependencies for tabulate to our Docker and Conda environments.
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 Filter low-quality sequences by Nextclade QC status #144.
Modifies the script that makes a Markdown table of recent sequence
counts per clade to use a recency JSON constructed from all metadata per
lineage (instead of metadata for a specific tree) and the Nextclade
annotations on S3. This change allows us to report the clade counts for
all recently submitted sequences instead of limiting our report to
sequences that appear in a given tree.
Related to #130
Adds a prototype script that produces derived haplotype strings per
record from a given Nextclade annotations file with columns for clade
and mutations relative to each clade. The derived haplotypes produced
with this script could eventually replace the haplotypes we build from
the mutation-annotated trees and allow us to calculate haplotype
frequencies from all available data instead of a subset of data used to
build a tree.
Related to #130
Depends on nextstrain/nextclade#1492
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.
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