Residual README.md Changes From PR #30 (Root: Issue #26)

[ankushkgupta2]

Description

Please Describe the Bug(s) Fixed and/or the Feature(s) Added:

1. Changed 'Non-Scicomp' heading to 'Non-CDC' heading
2. Made the environment setup section clearer for those that are CDC users using Scicomp vs not and which corresponding steps to take
3. Within the non-CDC and Scicomp sections environment setup, further explained two paths: (1) which steps to take for creating entire tostadas environment (enables you to have all packages to run the individual python scripts if you desire) or (2) simply installing Nextflow by itself locally for non-CDC or initializing the nextflow module for CDC users, in order to only to use the NF wrapper (will be most users)
4. Removed the Monkeypox Gitlab URL

Checklist

Go Through Checklist Below and Place A ✔️ if Completed

General Checks

• Have you ran appropriate tests (unit/integration/end-to-end) to check logic across run environments (Conda/Docker/Singularity on Scicomp/AWS/NF Tower/Local)?

  For each relevant configuration:

  • Can the program run completely through without erroring out?
  • Does it produce the expected outputs, given the inputs provided?

• Have you conducted proper linting procedures?

  • Numpy formatted docstrings for functions
  • Comments explaining lines of code
  • Consistent and intuitive naming conventions for variables, functions, classes, methods, attributes, and scripts
  • Single empty line between class functions, two lines between non-class functions, and two lines between imports and code body
  • Camel case formatting for class names

• Have you updated existing documentation (README.md, etc.) or created new ones within docs?

CDC Checks

• Did you check for sensitive data, and remove any?
• Are additional approvals needed for this change?
• Are there potential vulnerabilities or licensing issues with any new dependencies introduced?
• If you added or modified HTML, did you check that it was 508 compliant?