[TheiaCoV ONT] Update Artic to 1.9.0

[xonq]

This PR closes #

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

🧠 Summary

⚡ Impacted Workflows/Tasks

Workflows

Δ theiacov_clearlabs

Δ theiacov_ont

Tasks

Δ consensus

Δ read_filtering

This PR may lead to different results in pre-existing outputs: Yes/No

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

🛠️ Changes

• primer schemes are included in Artic by default and can be accessed by the user
• medaka model changed to clair3 and the best model selected by default
• table of comparative evaluation of assembly quality

⚙️ Algorithm

➡️ Inputs

theiacov_ont +1 -1

+ consensus.clair3_model
- consensus.medaka_model

theiacov_clearlabs +2 -2

+ artic_docker
+ consensus.clair3_model
- consensus.medaka_model
- medaka_docker

⬅️ Outputs

theiacov_ont +2 -3

+ artic_pipeline_reference
+ clair3_vcf
- medaka_reference
- medaka_vcf
- read1_trimmed

theiacov_clearlabs +2 -2

+ artic_pipeline_docker
+ artic_reference
- artic_docker
- medaka_reference

🧪 Testing

• freyja_fastq

  read_filtering
• theiacov_clearlabs

  consensus, theiacov_clearlabs
• theiacov_ont

  consensus, read_filtering, theiacov_ont
• theiaeuk_ont

  read_filtering
• theiaprok_ont

  read_filtering

Suggested Scenarios for Reviewer to Test

🔬 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 and follow the documentation style guide
  • You have updated the "Last Known Changes" field for any affected workflows in the respective workflow documentation page and for the entry in the docs/assets/tables/all_workflows.tsv table to be the tag for the next upcoming release. If you do not know the tag, please put "vX.X.X"

🎯 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 and adheres to the documentation style guide