Add benchmark to the Snakemake style guide

[joverlee521]

Description of proposed changes

Makes it so much easier to identify bottlenecks in workflows if they all just start out with benchmarks!

Related issue(s)

Prompted by nextstrain/ncov-ingest#446

Checklist

• Checks pass

[joverlee521]

Read the Docs failure related to #209

[corneliusroemer]

I personally dislike the benchmark directive as it adds noise and I never use it, one can just look at logs to see which steps take long - it'd be better if there was a snakemake option to enable benchmarks that didn't add 2 lines to each rule.

Prior discussion:

• Benchmark in every rule is annoying - extra 2 lines that should not be necessary ncov-ingest#472

Related snakemake issues/PRs:

• Easy way to benchmark all rules snakemake/snakemake#50
• Feature requests: benchmark command line option snakemake/snakemake#561
• Benchmark for entire workflow snakemake/snakemake#764
• feat: global benchmark options snakemake/snakemake#2176

[joverlee521]

Benchmarks are one of those things that are not used often, but are extremely helpful to have for optimizing workflows. It's nice when they are generated every run so that we have base stats for comparisons. They are especially useful since Snakemake got rid of the --stats flag. For example, benchmarks were used by @victorlin in ncov, @j23414 in norovirus/dengue, and most recently @kimandrews in tb work.

We can potentially remove this recommendation from the docs and remove the benchmark directives from workflows once the global benchmark option is available in Snakemake, but for now it seems more beneficial to keep if the only downside is adding 2 extra lines per rule.

[victorlin]

+1 on what Jover said, but I get the frustration. It seems like most of the recommendations in our style guide exist to work around less-than-ideal default behavior of Snakemake.