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nextstrain / seasonal-flu

Scripts. config, and snakefiles for seasonal-flu nextstrain builds
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Upload metadata.tsv for downstream use #107

Closed corneliusroemer closed 1 year ago

corneliusroemer commented 1 year ago

You already upload raw fasta to AWS in rule upload_sequences.

It would be useful for our https://github.com/neherlab/flu_frequencies repo to be able to download metadata.tsv as produced by your rule parse.

I will duplicate your parse for now, but in the future it would be nice to reduce code duplication and parse in one place.

Is there a reason you are currently only uploading the raw data not the parsed one?

huddlej commented 1 year ago

Thank you for asking about this, @corneliusroemer. There's no good reason to not upload sequences.fasta and metadata.tsv now. The only reason I didn't originally was because I wasn't sure whether the S3 uploads would be useful or how they would work. Now that they are working, we can upload the more useful downstream files.