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nextstrain / ncov-ingest

A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.
MIT License
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Add benchmark and `--stats` #451

Closed joverlee521 closed 3 months ago

joverlee521 commented 3 months ago

Description of proposed changes

Add benchmark for all Snakemake rules and use --stats to get more data for #446.

I plan on merging tomorrow morning before the automated workflow runs at ~11am PT.

Related issue(s)

Resolves #240 Gathering stats for #446

Checklist

joverlee521 commented 3 months ago

I love benchmarks! +1 for their inclusion in our Snakemake style guide, @joverlee521.

I merged https://github.com/nextstrain/docs.nextstrain.org/pull/210 yesterday, but it's not available in our latest docs yet because RTD build is currently failing