Submission fasta reroute ick4

[jessicarowell]

Description

For multicontig fasta submission, add -M n -Z flags to table2asn if fasta contains multiple headers.
Change submission_ch after bakta process to replace original fasta with the annotated fasta for submission.
Also, emit .fna after RUN_BAKTA process.
Corrections to modules.config publishDirs and removes some extraneous publishDir commands within local modules (because they're already in modules.config).

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: