John Huddleston

icon indicating a website link http://huddlej.github.io/ icon indicating an email [email protected]

icon company @blab @nextstrain icon location Staff scientist in @blab at Fred Hutchinson Cancer Center studying predictive models of influenza evolution.

Results 96 comments of John Huddleston
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[REVIEW]: Snk: A Snakemake CLI and Workflow Management System

@danielskatz Thank you for checking! I would like the open issues to be addressed before publication, even if they are addressed with a comment that they are out of scope....

[REVIEW]: Snk: A Snakemake CLI and Workflow Management System

@danielskatz I checked the final remaining box in my checklist, based on @Wytamma's responses to the issues linked above. Happy to see this published!

Use Nextclade to assign clade labels in main phylogenetic workflow

We recently [added logic to the phylogenetic workflow to support running Nextclade on all sequences](https://github.com/nextstrain/seasonal-flu/pull/240#issuecomment-3140940748). This change allowed us to filter sequence by their QC annotation, but it also allows...

[BUG] augur mask only supports VCFs with a single "chromosome" entry

Yeah, if there were a "very low priority" tag, this issue would have it, but I wanted to document the edge case somewhere so it didn't get lost forever. That...

`parse` silently removes spaces from record ids in the sequence output but not in the metadata output

> Why modify names at all? The FASTA format technically* doesn't allow spaces in the record id, since a space is used to delimit the record id and description in...

`parse` silently removes spaces from record ids in the sequence output but not in the metadata output

@genehack and I were just chatting about this again and it seems like an ideal long-term solution would be to limit the scope of `augur parse` to _only_ parsing FASTA...