seasonal-flu
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nextstrain
Scripts. config, and snakefiles for seasonal-flu nextstrain builds
I originally plotted counts of HA sequences by lineage and region with altair, with the plan to make the figure interactive. However, we end up most often including these figures...
## 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...
### Current Behavior [Our current approach to joining segment-level metadata records into isolate-level metadata records](https://github.com/nextstrain/seasonal-flu/blob/d8bca3a5359c08d7a47522b3fe7fdee5f12c8b25/workflow/snakemake_rules/select_strains.smk#L49-L71) is an HA-centric one such that NA records without a matching HA do not get...
Currently, when a [private nextflu build](https://github.com/nextstrain/seasonal-flu/actions/workflows/run-private-nextflu-builds.yaml) completes, we have to manually trigger the [deploy private nextflu](https://github.com/nextstrain/seasonal-flu/actions/workflows/deploy-private-nextflu.yaml) workflow with the AWS Batch job ID. Now that the GH Action job stays...
I am trying to run the nextstrain pipeline, I did following steps but I am getting an error. Step 1. I downloaded seasonal-flu repo and created a directory called "data/h3n2",...
Fixes https://github.com/nextstrain/seasonal-flu/issues/155 Interestingly, we don't have any entries for "Suffolk" in the fauna/source-data/geo_synonyms.tsv¹ and I couldn't find any metadata in our private S3 bucket that includes "Suffolk" as a location....
### Current Behavior In the `lat_longs.tsv` file, Suffolk points to somewhere in Boston Harbor. ### Expected behavior "Suffolk" should point to somewhere in the East of England/East Anglia, not too...
## Description of proposed changes Add measurements panel to H3N2 HA build for Welsh et al. escape scores grouped by serum or cohort. Enables interactive visualization and filtering of data....
## Context Despite our myriad quality filters in the workflow including a global clock rate filter, local clock rate filter, an outliers list, and dropping sequences with poor alignments, our...
## Context We currently assign clade labels to trees in our main phylogenetic workflow using the `augur clades` command and the influenza clade nomenclature TSVs. However, clade assignments vary for...
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Scripts. config, and snakefiles for seasonal-flu nextstrain builds