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Add measurements panel in nextflu-private builds #81

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@huddlej huddlej commented Apr 19, 2022

Description of proposed changes

Adds a new Snakemake file, Snakefile_nextflu, that mirrors Snakefile_WHO and adds logic to build measurements JSONs for HA-based builds with the new augur measurements command. The current prototype only works for H3N2. These builds would only be pushed to the nextflu-private Nextstrain Group.

We should decide as a team whether to proceed with this kind of implementation for now or to first test and merge the refactored workflow. The refactored workflow might be better suited for managing separate live and private builds. Our decision here should be part of a bigger plan to sunset the private nextflu site.

Testing

Tested locally with the following command:

snakemake \
  -p \
  --use-conda \
  --conda-frontend mamba \
  -j 4 \
  --snakefile Snakefile_nextflu \
  auspice-nextflu/flu_who_h3n2_ha_2y_cell_fra.json \
  auspice-nextflu/flu_who_h3n2_ha_2y_cell_fra_tip-frequencies.json \
  auspice-nextflu/flu_who_h3n2_ha_2y_cell_fra_measurements.json

auspice view --datasetDir auspice-nextflu

Adds a new Snakemake file that mirrors `Snakefile_WHO` and adds logic to
build measurements JSONs for HA-based builds with the new `augur
measurements` command [1]. The current prototype only works for H3N2.

[1] nextstrain/augur#879
@huddlej huddlej marked this pull request as draft April 19, 2022 21:37
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huddlej commented Dec 28, 2022

Closed in favor of #76

@huddlej huddlej closed this Dec 28, 2022
@huddlej huddlej deleted the add-measurements-panel branch December 28, 2022 21:33
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