[TheiaCoV] Reorder flu segments from largest to smallest in irma task

[Michal-Babins]

This PR closes #630

🗑️ This dev branch should be deleted after merging to main.

🧠 Summary

PR updates TheiaCoV workflow for when "flu" organism is chosen, and reorders flue segments from largest to smallest in the irma task.

⚡ Impacted Workflows/Tasks

wf: TheiaCov
task: task_irma

This PR may lead to different results in pre-existing outputs: Yes

This PR uses an element that could cause duplicate runs to have different results: Yes/No

🛠️ Changes

Changes take expected flu segment lengths (large to small) and concatenates them in the irma task to the irma consensus fasta in descending order

⚙️ Algorithm

In task_irma.wdl for the flu track of TheiaCoV, the process for creating the consensus fasta was updated to order the flu segments from largest to smallest segments=("PB2" "PB1" "PA" "HA" "NP" "NA" "MP" "NS") as per request, updating the assembly_fasta output.

➡️ Inputs

⬅️ Outputs

• assembly_fasta (when flu track is triggered)

🧪 Testing

This PR was tested against flu data found in the flu_testing table here. The workspace for testing this data can be found here.

Further testing was done on the theiacov validation set against WNV and MPXV

Suggested Scenarios for Reviewer to Test

Test with flu set from flu_testing table here. For flu ensure output fasta are in the following order of segments: segments=("PB2" "PB1" "PA" "HA" "NP" "NA" "MP" "NS"). Test with validation sets of your choosing.

🔬 Final Developer Checklist

• The workflow/task has been tested and results, including file contents, are as anticipated
• The CI/CD has been adjusted and tests are passing (Theiagen developers)
• Code changes follow the style guide
• Documentation and/or workflow diagrams have been updated if applicable (Theiagen developers only)

🎯 Reviewer Checklist

• All changed results have been confirmed
• You have tested the PR appropriately (see the testing guide for more information)
• All code adheres to the style guide
• MD5 sums have been updated
• The PR author has addressed all comments
• The documentation has been updated