fixed channel mixup and removed remnants of utility function

[kyleoconnell]

Description

did more work to fix the channel mismatch, seems to be fixed. Now the reads_ch is meta.id, fasta, fastq1, fastq2 so I also modified the annotation modules to accomdate this longer tuple, although it doesn't change the process in practice.

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?

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