Use augur merge for sequences

[victorlin]

Description of proposed changes

Use our own tooling designed for this type of operation.

Related issue(s)

• Use augur merge to spike in USVI records #73

Checklist

• Tested locally
• Checks pass
• Merge base PR Use augur merge #75
• Merge and release merge: Support sequences with cross-checking augur#1601

[jameshadfield]

This seems clear-cut for unsegmented pathogens, whereby we have a single augur merge command which collects all n metadata TSVs & m sequence FASTAs into a single TSV & FASTA.

For segmented genomes our analyses use a single TSV and 1 FASTA per segment. So the metadata includes samples which may be in only one FASTA (e.g. only one segment was sequenced). AFAIK we haven't got prototypes for how to merge multiple inputs for segmented pathogens beyond my prototype in avian-flu which handles metadata merging and sequence merging independently. It's not clear what's the best approach here.

We could continue to treat things independently. When augur merge is given both sequences & metadata does it do more than drop rows?

Should augur merge be aware of segments? e.g. you could specify something like --sequences usvi=seg1=<path> usvi=seg2=<path>.

[victorlin]

@jameshadfield thanks for bringing that up. Replied in nextstrain/augur#1579 (comment)