John Huddleston

Thank you @cjw85 and @ivan-aksamentov! I've [added support for x86 OS X in a PR](https://github.com/bioconda/bioconda-recipes/pull/26919). If this goes through, I'll add support for arm64 OS X, too.

CI fails on the "push" because this PR branches from the workflow with the old Nextalign/Nextclade commands, but the CI runs with the latest Docker image using new Nextalign/Nextclade: ```...

With the boolean-valued approach, I was actually imagining omitting the argument from the shell completely when the value is `False`. This would work the same way we optionally include a...

This issue has been partially resolved by #633. Documenting all available `config.yaml` options is outside of the scope of our documentation, since these options depend directly on Snakemake's documentation. We...

@jacaravas Just to clarify, is the data flow for the metadata you pass to sanitize metadata like this? 1. GISAID API endpoint 2. internal database 3. metadata TSV

@emmahodcroft, is there any value to merging this now (after resolving conflicts) or is it too late to matter much? (I'm trying to clean up old PRs.)

Thanks for trying this out, @jameshadfield! I ran into the same issue with a Nebraska-focused tree (N=~1000 strains). Adding `-safe` initially worked as expected, although IQ-TREE printed a bunch of...

FWIW, I stumbled on [Rob's analysis that led him to suggest this very small minimum branch length](https://github.com/roblanf/sarscov2phylo/blob/master/tree_estimation2.md#iteration-13). His context (analyzing 40,000+ sequences) and Nextstrain's (analyzing ~4,000 sequences) are pretty different....

I think @jameshadfield is right on here about this being an ncov-specific problem. [Amino acid mutations come from the translated alignments that happen from nextalign](https://github.com/nextstrain/ncov/blob/38dea66868fe5e26f0b7231b9ac710a7e5e2a82e/workflow/snakemake_rules/main_workflow.smk#L898-L902) and then [ancestral state reconstruction...

Thank you both for pointing this out! I imagined we could support piping between these commands, as a minimal way to support composing transforms. I just updated the issue to...