John Huddleston

Locally resolving #273 by adding the missing column to the metadata did not fix the workflow because there are still several hardcoded columns in other rules or scripts of the...

I'm sorry I missed this when you first posted about it, @jameshadfield, but this is a super useful feature/resource! I wasn't sure which pathogens we actually had public data for...

@sekhwal and I met today to walk through the workflow and figure out where his local sequence was getting dropped. We found that it was dropped at the "flag outliers"...

Additional considerations: - Do we want to rewrite the whole workflow from scratch or refactor the existing workflow? - Should we continue to consider the WHO builds as a separate...

Great catch! Would it be reasonable to update [the calculation of branch lengths in nextflu](https://github.com/blab/nextflu/blob/b4bd055eb853a181215b7df0685691427236783b/auspice/js/auspice/tree_functions.js#L58) to use the `branch_length` attribute we export in the auspice JSONs instead of the missing...

During issue triage we also realized that this guide can be updated to use Nextstrain open data.

Related issue from back when "nextclade" was called "nextalign": https://github.com/nextstrain/augur/issues/706

I know both @trvrb and @rneher have requested this functionality, but I don't fully agree that `augur align` _should_ wrap `nextclade`. My main reasons are: 1. `augur align` has historically...

## Review checklist for @huddlej ### Conflict of interest - [x] I confirm that I have read the [JOSS conflict of interest (COI) policy](https://github.com/openjournals/joss/blob/master/COI.md) and that: I have no COIs...

@danielskatz @Wytamma I'm finished reviewing the paper and software. It was a pleasure to try out this new tool. There are many times in the last decade that I wish...