james hadfield

Hi Eric - the common way to do this is to [fork the repo and submit a PR from your fork](https://jarv.is/notes/how-to-pull-request-fork-github/). Thanks in advance for your contribution!

This would be a big improvement. The sanitize metadata script [already has code](https://github.com/nextstrain/ncov/blob/master/scripts/sanitize_metadata.py#L235-L249) for inferring the column representing "strain", would requiring this to be present in all files be too...

How many sequences are you running [0] and how much memory do you have [1]? IQ-TREE has died due to a Segmentation fault, so my guess is that you've run...

You're broadly correct that TreeTime is the bottleneck currently and there are two avenues we have discussed: (1) There's discussion in the [treetime repo](github.com/neherlab/treetime) about various ways to speed this...

One limitation of the current ncov workflow (and nextstrain more generally) is that _all_ custom colours have to be specified in one file to be passed to `augur export`. For...

@abattenhouse can you try using the following format in the YAML ```yaml # Subsampling parameters subsampling: your_scheme_name: your_sample_name: min_date: "--min-date 2000-01-01" max_date: "--max-date 2002-01-01" ``` Similar issue: https://github.com/nextstrain/ncov/issues/644#issuecomment-849946060 Reference docs:...

cc @joverlee521 -- This content is indeed hardcoded in auspice.

Leaving this issue here as it's natural to file it to this repo but locking it as it's not specific to hCoV-19. https://github.com/nextstrain/nextstrain.org/issues/130 is the issue to bring proper language...

> With the boolean-valued approach, I was actually imagining omitting the argument from the shell completely when the value is `False`. 👍

I'm not quite sure what you mean here -- are you asking for a visualisation where internal nodes (branches) are coloured according to the proportion of descendants they have? Currently...