Trevor Bedford

`vdb/dengue_sequences` has authors in format of `Corwin et al.`, `Dewi et al.`, etc... Zika, Ebola, etc... have authors in format of `Mlakar et al`. The presence of the `.` is...

I didn't like how in the the live version we have a mixture of "clades" like `MPXV Clade 1` and "lineages" like `B.1` and we call all of this "Clade"....

Core builds should all have matching repos

10

"Core" builds on nextstrain.org (those that appear as primary tiles) are builds maintained by the Nextstrain dev team. Each of these core builds should have a matching GitHub repo under...

Epitope and non-epitope coloring for H1N1pdm NA broken

1

Currently, epitope (`ep`) and non-epitope (`ne`) coloring for H1N1pdm NA is broken: * https://nextstrain.org/flu/seasonal/h1n1pdm/na/2y?c=ep * https://nextstrain.org/flu/seasonal/h1n1pdm/na/2y?c=ne

Include profile for open 21L builds

1

## Description of proposed changes This PR copies the logic in `nextstrain_profiles/nextstrain-gisaid-21L/` to `/nextstrain_profiles/nextstrain-open-21L/`. Specific gisaid vs open changes etc... were derived by diffing the existing `nextstrain-gisaid` vs the existing...

Elevate lineage XDV.1 as clade 24D

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With this PR, we are designating clade 24D (lineage XDV.1) #### Clade 24D, lineage XDV.1 Clade 24D, lineage XDV.1 stems from a rather complex recombination event. XDV is officially a...

Improve / standardize the way that we pass through default parameters and build-specific parameters

5

## Context Currently, the workflow is a bit of mess when it comes to how one can specify parameters. There seems to be 3 different approaches: ### 1 – parameters.yaml...

## Description of proposed changes This PR is attempting to solve the same problem as #1129, but in a different fashion. In this case, we keep the subsampling in the...

## Description of proposed changes This is a bug fix PR. There was a bug in the current behavior where the rule `frequencies` was calling `config["frequencies"]["narrow_bandwidth"]`. This resulted in --narrow-bandwidth...