John Huddleston

Thanks, @thienktran! That's basically what we need; all that's missing is a wide-to-long transform on that output to match the format expected by @marlinfiggins's models. From antigen output this would...

It seems like we should just minify all JSONs by default. Inspecting JSONs with [jq](https://stedolan.github.io/jq/) is an easy way to make them human-readable when you need to debug something and...

Along these same lines, we don't have an option to minify frequencies JSONs which can also get really annoyingly big.

I just reinvented the wheel a bit in the seasonal flu repo with [a similar command to generate a custom color scale in an Auspice config JSON](https://github.com/nextstrain/seasonal-flu/blob/68dbe2c21dea858d5db783cc3a065b6f14428e0c/scripts/generate_scale_for_coloring.py). Thanks to @joverlee521...

Thank you for testing this and confirming it works, @j23414! > I might be lacking context here, but do we need to account for these GISAID downloads that do have...

Ah, got it. Thank you for checking this, @j23414! I forgot that path did not allow replacing spaces with underscores. That suggests that the original code in sanitize metadata was...

This is a great summary of our conversation yesterday! > can multiple sera be represented by a single distance map? Multiple sera can only be represented with an aggregate metric...

@corneliusroemer The exclude-where/include-where syntax was never designed to be a full-featured query syntax, but you could use the `--query` interface which supports pandas-style query syntax to select the records you...

@rneher's point above makes it clearer to me how we could do this without touching TreeTime internals. Thinking through the user experience of asking `augur refine` to `--remove-root`, though, it...

There is [an ancient (2-year-old now) PR](https://github.com/nextstrain/ncov/pull/611) that does something similar but only when the workflow errors. Checking preemptively seems maybe better, though.