Jover Lee

Bumping this PR since we've had people as about this in our discussion forum ([1](https://discussion.nextstrain.org/t/overriding-tree-builder-args/1051), [2](https://discussion.nextstrain.org/t/getting-node-support-values-in-the-ncov-workflow/1200)).

@jameshadfield Should the hardcoded bit be completely removed from auspice and just injected through nextstrain.org?

Ah, behavior on staging is a little weird (maybe intentional?) in that you have to provide the _exact_ url to the dataset. Since the builds are now split into different...

FYI, I built the [monkeypox/ingest transform rule](https://github.com/nextstrain/monkeypox/blob/4efcde7473d1fd61bf482936826e3d07f26d407b/ingest/workflow/snakemake_rules/transform.smk#L40-L68) as a prototype for this proposed subcommand. The shell pipeline connects small Python scripts that all read NDJSON records from stdin and then...

@jameshadfield The examples you've listed seem like very general CSV/TSV manipulations that can be done with other tools (e.g. [tsv-utils](https://github.com/eBay/tsv-utils) or [csvtk](https://github.com/shenwei356/csvtk)). I don't think we want to reinvent the...

Thank you for the detailed examples @huddlej! I fully support the I/O options for individual commands especially to make one-off calls easier for users. With that in mind, the `augur...

In a similar vein of UX cost, I was thinking that each individual command should normalize strings in addition to the `normalize-strings` command. Ideally, an `augur curate` chain would start...

Dumping some thoughts/questions here after talking more about the I/O framework with @tsibley today. --- If a user provides both a metadata TSV and a FASTA file as inputs, I...

Thank you for the feedback @ammaraziz! >When you refer to `record` do you mean data in the fasta file, the metadata row entry or both? I think there needs to...

Hmm, starting with pandas 1.4.0, they [only support Python 3.8 and higher](https://pandas.pydata.org/docs/whatsnew/v1.4.0.html#increased-minimum-version-for-python). Maybe we should just work around it to avoid bumping the minimum Python dependency for Augur.