[External] [Feature] Running Variola Sequences through Pipeline

[jtakakuwa]

What is the Feature Related To? Please Provide a Description.
The pipeline needs to be adjusted to run variola samples through the annotation and submission process. Portions of the script with mpox-specific parameters need to be adjusted to allow it to run with variola.

Place an ❌ in a Box that Best Matches the Feature's Importance:

• [] 1 - Most important (absolutely integral and will not use codebase at all without it)
• 2-4 - Moderate (still using codebase for other functions but is serving as a blocker for future use-cases)
• [] 5 - Least important (would like to see but there are no stringent expectations nor urgency for current/future use-cases) 

Any Additional Context or Information? Has There Been Any Progress Made So Far Towards this Request? Any Helpful Resources to Reference? Screenshots or Links?

1. Initial testing with the variola reference genome as a sample as well as a fasta with seven different
   variola samples. Both tests pass the validate parameters, cleanup files and metadata validation steps.
   However, they both fail the liftoff annotation process. This was resolved by changing the FASTA files from ASCII text to ASCII text with very long lines (producing a single-line FASTA, with header and sequence).

Error resolved by 1:

2. Testing proceeds, the pipeline still fails at the liftoff stage. The variola reference was changed to include repeat_region, CDS and gene information. This resolved the current error but created a different error.

Error resolved by 2:

3. The traceback was used to find that the error was originating in the add_repeat_region_lines function in liftoff_submission.py. This function was commented out, which allowed successful processing of the variola sample.

Error resolved by 3:

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