reichlab / variant-nowcast-hub

A repository to store COVID-19 variant nowcasts collected as a modeling hub.

reichlab/variant-nowcast-hub Issues

Dockerize the variant data pipeline
Updated a month ago1
Determine pipeline behavior when/if any downloaded sequences do not have corresponding metadata
Updated 2 months ago
use root sequence obtained via nextstrain
Updated a day ago1
catch and fail early on errors in downloading data
Updated a month ago1
Add support to specify the start and end of a date range for sequence collection dates
Updated a month ago3
pull run settings out into a config file and/or allow them to be specified as command line arguments
Closed a month ago1
more graceful handling of error when `"root_sequence"` key is not found in `reference_data`
Closed a day ago2
Consider changing sequence data filter for initial data pull from `--updated-after` to `--released-after`
Closed a month ago3
functionality to merge metadata and clade assignment outputs
Closed 2 months ago1
Support for historical versions of reference trees (along with their corresponding root sequence)
Closed 2 months ago1