build/run: Add Snakemake's `--benchmark-extended` as a default flag

[joverlee521]

Prompted by nextstrain/docs.nextstrain.org#210 (comment), I was reading Snakemake docs on benchmarks and realized there's a new --benchmark-extended flag

Since version 8.11.0, it is possible to have extra benchmark metrics with the command --benchmark-extended:

jobid: Internal job ID,

rule_name: Rule name,

wildcards: Job wildcards,

params: Job parameters,

threads: Number of threads requested for this job,

cpu_usage: Total CPU load,

resources: Resources requested for this job,

input_size_mb: Size of input files (MiB),

The extra benchmark metrics seem nice to have for debugging across all of our workflows that I'm tempted to add it as a default flag for our nextstrain build and nextstrain run commands. nextstrain run does not take additional Snakemake flags, so we must add it in the CLI to support the extra benchmarks. nextstrain build does accept Snakemake flags, so the alternative is to add the --benchmark-extended flag to the nextstrain build invocations in GH Actions.

[victorlin]

This seems useful. I tested locally with Snakemake 9.9.0 and --benchmark-extended seems to have no effect for rules without benchmark directives, which is good for compatibility if added as a default flag.

[victorlin]

I started implementing this in #513, but CI failed in the ambient runtime check which is still using Snakemake v7:

snakemake: error: unrecognized arguments: --benchmark-extended

Options, roughly sorted from least to most code changes:

1. Don't worry about backwards compatibility with Snakemake <8.11.0 and release the feature in the next major version of Nextstrain CLI.
2. Only add it for managed runtimes, where we can add an entry to IMAGE_FEATURE then only add --benchmark-extended if the runtime version is known to include Snakemake ≥8.11.0.
3. First parse the version from snakemake --version then only add --benchmark-extended if the version is ≥8.11.0.

Leaning towards option 2.

[jameshadfield]

Conceptually no. 2 seems the best option, especially since #513 is very readable.

[joverlee521]

Agree, seems reasonable to go with option 2.