Update core analysis docs

[cbethell]

Issue Addressed
Closes #275, #274, and #263

What is the purpose of these changes?

This PR makes the recommended updates to the main README.md file in preparation for further usability evals.

What changes did you make?

The following changes are made in this PR:

• the main steps of setting up and running the workflow are numbered for easier interpretation (Number the preparation steps of the core workflow #275)
• emphasis is placed on the parts of the example commands that users would need to replace (Emphasize the parts that user will need to replace in example commands #274)
• the minimum Snakemake version is noted as determined by tracking the changelog and the PR filed to update Snakemake's documentation (Note minimum snakemake version that is required in the documentation #263)
  Were there any other solutions that you tried?

Any comments, concerns, or questions important for reviewers

Do these changes seem to adequately address the issues mentioned/tagged above?

Checklist

Place an x in all boxes that you have completed.

• I have run the most recent version of the code
• If I am adding in reports or generating any plots, I have reviewed the necessary reports
• I have added all necessary documentation (if applicable)

[allyhawkins]

I think rather than changing to the all caps, underscore separated paths in the examples, we should include notes about what the individual arguments represent and then a reminder to replace the paths in bold immediately under the command. I think by explicitly stating it we might get through to more people and we should be sure to explain what each option actually represents.

[allyhawkins]

I actually think I would remove the underscores in between the words. I'm also not crazy about the all caps, but maybe that will draw people's attention to it.

I also think you want to add a few sentences below that state: "Where config_results_dir is the relative path to the results directory where all results from running the workflow will be stored". And then do the same for the project metadata.
We do something similar in scpca-nf - https://github.com/AlexsLemonade/scpca-nf/blob/main/external-instructions.md#configuring-scpca-nf-for-your-environment

[cbethell]

I've implemented your suggestions to add a line or two explaining the parameters and bolding/emphasizing the need to replace with the relevant filepaths @allyhawkins -- I did keep the CAPS since that was an original suggestion from Deepa but agree that the underscores were much so I removed them. Let me know what you think now!

[allyhawkins]

This looks good! Just one sentence order switch, but no need for me to look at it again.