Update master

[jessicarowell]

Description

All the v8.1.1 changes

1. updated params.species in the bacteria.config and virus.config files
   in create_batch_tsvs.py, maybe pd.read_excel skip the first (mostly blank) row and read the second row as the header
2. minor formatting fixes in genbank.nf
3. major updates to documentation including streamlining, adding Quick Links to landing page, correcting some links, and 4. removing some unnecessary files
4. enforce submit.ready trigger file to always be uploaded last

Checklist

Go Through Checklist Below and Place A ✔️ (X Inside the Box) if Completed

General Checks

• [] Have you run 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?
• [] If you added or modified HTML, did you check that it was 508 compliant?

Are additional approvals needed for this change? If so, please mention them below:

Are there potential vulnerabilities or licensing issues with any new dependencies introduced? If so, please mention them below: