Remove nextstrain_profiles/nextstrain-country

[joverlee521]

From discussion below, we've decided to just remove rebuild_country.yml + nextstrain_profiles/nextstrain-country since they are not actively being used

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Context

I originally flagged this in #1119 (comment):

I don't think this profile ever worked as intended, since the build names have three parts delimited by underscores (e.g. nextstrain_country_1m), while our auspice config rule only expects two parts:

ncov/workflow/snakemake_rules/export_for_nextstrain.smk

Lines 145 to 146 in eb488d6

	if "_" in build_name:
	build_region, build_timespan = build_name.split("_")

Possible solutions

Easiest change would be to switch build names from nextstrain_country_1m to country_1m. However, this would change Auspice JSON file names which would change the build URLs on nextstrain.org

TODOs

• update build names from nextstrain_country_1m to country_1m
• enable rebuild-country.yml workflow

[joverlee521]

However, this would change Auspice JSON file names which would change the build URLs on nextstrain.org

I cannot find any builds in s3://nextstrain-data with the nextstrain_country_<time> name so maybe this is a non-issue?

@trvrb, could you comment on whether the proposed change would affect your work? I think you might be the only one who has used this profile?

[victorlin]

If there's no evidence that rebuild_country.yml + nextstrain_profiles/nextstrain-country are actively used, I'd vote to remove them (as briefly mentioned in #1119 (comment))

[joverlee521]

Asking for feedback on Slack

[trvrb]

I haven't used this in a long while (I'm not even sure it was ever working correctly). I do think it's good functionality to be able to look at what's circulating in a particular country. This would be for one-off analyses that are not uploaded to data.nextstrain.org. It's generally not currently much of a priority for this to be working. I'd be okay with it being cut out if it's not working.

[joverlee521]

Thanks for the feedback! I'll just remove rebuild_country.yml + nextstrain_profiles/nextstrain-country then.