User provided annotations for genbank submission

[kyleoconnell]

Description

Added column to metadata to get gff path as optional input, user needs to skip annotation if they supply gffs or this will fail.

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:

[jessicarowell]

If you run --annotation true it will run it but still submit user-provided gff file (not the one generated by the pipeline)