Add benchmark and --stats
#451
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Adding as part of #240 to help collect more data for tackling #446. One unexpected behavior that I ran into when testing the `--stats` option is that Snakemake doesn't generate the stats file if the workflow exits with an error at any step. Note that the Snakemake `--stats` option is not available starting with Snakemake v8, so this will need to be removed when we eventually upgrade Snakemake in our runtimes.
The use of `shellquote` was removed in 2dab1f9.
Per Nextstrain's Snakemake style guide, using the `message` directive overrides the default Snakemake outputs which includes other critical details. <https://docs.nextstrain.org/en/latest/reference/snakemake-style-guide.html#avoid-the-message-rule-attribute>
huddlej
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Jun 18, 2024
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I love benchmarks! +1 for their inclusion in our Snakemake style guide, @joverlee521.
I merged nextstrain/docs.nextstrain.org#210 yesterday, but it's not available in our latest docs yet because RTD build is currently failing |
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Description of proposed changes
Add benchmark for all Snakemake rules and use
--statsto 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