[TheiaCoV] Update nextclade dataset tags and pangolin docker version

[Michal-Babins]

… parameters

This PR closes #669

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

🧠 Summary

This PR updates nextclade dataset tags to the latest versions as of 12/3/2024, as well as bumping the pangolin docker from 1.29 -> 1.31.

Aside, but along with this I made a utility to automatically check nextclade versions that need to be udpated.
https://github.com/theiagen/utilities/blob/mb-nextclade-utility/scripts/nextclade-version-check.sh

⚡ Impacted Workflows/Tasks

The wf_organism_parameters has been updated.

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

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

🛠️ Changes

The following changes have been made for latest updates:

Variable Name	Dataset Name	Latest Tag	Current Tag
sc2_nextclade_ds_name	nextstrain/sars-cov-2/wuhan-hu-1/orfs	2024-11-19--14-18-53Z	2024-07-17--12-57-03Z
mpox_nextclade_ds_name	nextstrain/mpox/lineage-b.1	2024-11-19--14-18-53Z	2024-04-19--07-50-39Z
h1n1_ha_nextclade_ds_name	nextstrain/flu/h1n1pdm/ha/MW626062	2024-11-27--02-51-00Z	2024-07-03--08-29-55Z
h3n2_ha_nextclade_ds_name	nextstrain/flu/h3n2/ha/EPI1857216	2024-11-27--02-51-00Z	2024-08-08--05-08-21Z
vic_ha_nextclade_ds_name	nextstrain/flu/vic/ha/KX058884	2024-11-05--09-19-52Z	2024-07-03--08-29-55Z
h1n1_na_nextclade_ds_name	nextstrain/flu/h1n1pdm/na/MW626056	2024-11-05--09-19-52Z	2024-07-03--08-29-55Z
h3n2_na_nextclade_ds_name	nextstrain/flu/h3n2/na/EPI1857215	2024-11-05--09-19-52Z	2024-04-19--07-50-39Z
vic_na_nextclade_ds_name	nextstrain/flu/vic/na/CY073894	2024-11-05--09-19-52Z	2024-04-19--07-50-39Z
rsv_a_nextclade_ds_name	nextstrain/rsv/a/EPI_ISL_412866	2024-11-27--02-51-00Z	2024-08-01--22-31-31Z
rsv_b_nextclade_ds_name	nextstrain/rsv/b/EPI_ISL_1653999	2024-11-27--02-51-00Z	2024-08-01--22-31-31Z

As well as bumping the pangolin docker:

us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.29 - -> us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.31

⚙️ Algorithm

Pangolin docker has been bumped from 1.29 -> 1.31.
Database versions for nextclade have been bumped for the latest versions available, as per the table above.

➡️ Inputs

No inputs have been changed.

⬅️ Outputs

No outputs have been changed.

🧪 Testing

TheiaCoV illumina PE has been tested here, Sars-cov-2, MPX, WNV, HIV, FLU + variants, rsv-a & rsv-b has been tested. All updated versions can be found in the nextclade_ds_tag.

Tested the following to ensure no issues with nextclade updates:
TheiaCoV_Fasta_PHB
TheiaCoV_Illumina_SE_PHB
TheiaCoV_Clearlabs_PHB
TheiaCoV_ONT_PHB

Please bring up any other scenarios you would like me to test.

Suggested Scenarios for Reviewer to Test

Please repeat the TheiaCoV_Illumina_PE test and check that all the organisms selected have the corrected update or NA. Feel free to test any of the other TheiaCoV variations.

🔬 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

[sage-wright]

Good to see that the pipefail stuff is actually working now which is why we're getting failures in some of those runs.

[sage-wright]

Thanks ⭐