…ersion of nanosim in the wrapper (#3648)

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This pull request leverages two things:

1. There are recent pre-trained models, generated with `nanosim` `3.2`,
which should be compatible with the latest versions of `nanosim` itself.
These come from these two pull requests:
  * bcgsc/NanoSim#224
  * bcgsc/NanoSim#238
2. In addition, we could patch the bioconda recipe for `nanosim` a bit
and update it to the latest version:
  * bioconda/bioconda-recipes#53528

With `scikit-learn` fixed to the version used for training those recent
models, we can now update this wrapper to use these latest models for
testing and the wrapper should in general work with those recent models.
 

### QC
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particularly ensure that:
* [x] `test.py` was updated to call any added or updated example rules
in a `Snakefile`
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<!-- This is an auto-generated comment: release notes by coderabbit.ai
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## Summary by CodeRabbit

- **New Features**
- Expanded simulation workflows with additional model inputs and updated
training datasets across genome, transcriptome, and metagenome
processes.

- **Chores**
- Upgraded `nanosim` dependency to version 3.2.3 and removed outdated
compatibility constraints for `numpy`.

- **Tests**
- Revised simulation output references in tests to align with the new
dataset paths and updated directory structures.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->