[TheiaCoV ONT and Clearlabs] Update consensus task container to artic:1.2.4-1.12.0

[cimendes]

This PR closes #595

🗑️ This dev branch should NOT be deleted after merging to main.

🧠 Summary

The previous container used, us-docker.pkg.dev/general-theiagen/staphb/artic-ncov2019-epi2me:latest was about 2 years out of date and no longer featured the latest medaka models. I've substituted it with us-docker.pkg.dev/general-theiagen/staphb/artic:1.2.4-1.12.0 which, besides being properly versioned, it includes the following models:

r103_fast_g507, r103_fast_snp_g507, r103_fast_variant_g507, r103_hac_g507,
r103_hac_snp_g507, r103_hac_variant_g507, r103_min_high_g345, r103_min_high_g360,
r103_prom_high_g360, r103_prom_snp_g3210, r103_prom_variant_g3210, r103_sup_g507,
r103_sup_snp_g507, r103_sup_variant_g507, r1041_e82_260bps_fast_g632,
r1041_e82_260bps_fast_variant_g632, r1041_e82_260bps_hac_g632,
r1041_e82_260bps_hac_v4.0.0, r1041_e82_260bps_hac_v4.1.0,
r1041_e82_260bps_hac_variant_g632, r1041_e82_260bps_hac_variant_v4.1.0,
r1041_e82_260bps_joint_apk_ulk_v5.0.0, r1041_e82_260bps_sup_g632,
r1041_e82_260bps_sup_v4.0.0, r1041_e82_260bps_sup_v4.1.0,
r1041_e82_260bps_sup_variant_g632, r1041_e82_260bps_sup_variant_v4.1.0,
r1041_e82_400bps_fast_g615, r1041_e82_400bps_fast_g632,
r1041_e82_400bps_fast_variant_g615, r1041_e82_400bps_fast_variant_g632,
r1041_e82_400bps_hac_g615, r1041_e82_400bps_hac_g632, r1041_e82_400bps_hac_v4.0.0,
r1041_e82_400bps_hac_v4.1.0, r1041_e82_400bps_hac_v4.2.0, r1041_e82_400bps_hac_v4.3.0,
r1041_e82_400bps_hac_v5.0.0, r1041_e82_400bps_hac_variant_g615,
r1041_e82_400bps_hac_variant_g632, r1041_e82_400bps_hac_variant_v4.1.0,
r1041_e82_400bps_hac_variant_v4.2.0, r1041_e82_400bps_hac_variant_v4.3.0,
r1041_e82_400bps_hac_variant_v5.0.0, r1041_e82_400bps_sup_g615,
r1041_e82_400bps_sup_v4.0.0, r1041_e82_400bps_sup_v4.1.0, r1041_e82_400bps_sup_v4.2.0,
r1041_e82_400bps_sup_v4.3.0, r1041_e82_400bps_sup_v5.0.0,
r1041_e82_400bps_sup_variant_g615, r1041_e82_400bps_sup_variant_v4.1.0,
r1041_e82_400bps_sup_variant_v4.2.0, r1041_e82_400bps_sup_variant_v4.3.0,
r1041_e82_400bps_sup_variant_v5.0.0, r104_e81_fast_g5015, r104_e81_fast_variant_g5015,
r104_e81_hac_g5015, r104_e81_hac_variant_g5015, r104_e81_sup_g5015, r104_e81_sup_g610,
r104_e81_sup_variant_g610, r10_min_high_g303, r10_min_high_g340, r941_e81_fast_g514,
r941_e81_fast_variant_g514, r941_e81_hac_g514, r941_e81_hac_variant_g514,
r941_e81_sup_g514, r941_e81_sup_variant_g514, r941_min_fast_g303, r941_min_fast_g507,
r941_min_fast_snp_g507, r941_min_fast_variant_g507, r941_min_hac_g507,
r941_min_hac_snp_g507, r941_min_hac_variant_g507, r941_min_high_g303, r941_min_high_g330,
r941_min_high_g340_rle, r941_min_high_g344, r941_min_high_g351, r941_min_high_g360,
r941_min_sup_g507, r941_min_sup_snp_g507, r941_min_sup_variant_g507, r941_prom_fast_g303,
r941_prom_fast_g507, r941_prom_fast_snp_g507, r941_prom_fast_variant_g507,
r941_prom_hac_g507, r941_prom_hac_snp_g507, r941_prom_hac_variant_g507,
r941_prom_high_g303, r941_prom_high_g330, r941_prom_high_g344, r941_prom_high_g360,
r941_prom_high_g4011, r941_prom_snp_g303, r941_prom_snp_g322, r941_prom_snp_g360,
r941_prom_sup_g507, r941_prom_sup_snp_g507, r941_prom_sup_variant_g507,
r941_prom_variant_g303, r941_prom_variant_g322, r941_prom_variant_g360,
r941_sup_plant_g610, r941_sup_plant_variant_g610

⚡ Impacted Workflows/Tasks

• TheiaCoV ONT
• TheiaCoV Clearlabs

This PR may lead to different results in pre-existing outputs: No if default model is not changed

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

🛠️ Changes

⚙️ Algorithm

No changes were made.

➡️ Inputs

No changes were made.

⬅️ Outputs

Made changes were made.

🧪 Testing

Local Testing

Tested on a sample from a FlowCell version 10.4.1

miniwdl run --task consensus /home/ines_mendes/Git/public_health_bioinformatics/tasks/assembly/task_artic_consensus.wdl samplename="CVL_026713_R" read1= artic_ncov2019_CVL_026713_R.fastq primer_bed= SARS-CoV-2.Midnight-ONT.V3.scheme.bed reference_genome= MN908947.fasta medaka_model="r1041_e82_260bps_hac_variant_g632" organism="sars-cov-2"

Testing on Terra

• TheiaCoV ONT
  • Several models r9 and r10: https://app.terra.bio/#workspaces/theiagen-validations/ines_sandbox/job_history/ba277c88-7ce1-40d9-a429-f9f380442a88 ✅
    • r1041_e82_260bps_hac_variant_g632
    • r941_min_hac_variant_g507
    • r941_min_high_g360 (default)
• TheiaCoV ClearLabs https://app.terra.bio/#workspaces/theiagen-validations/ines_sandbox/job_history/28abd69b-b793-4b73-86cc-c2014ddd190b ✅

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 (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

[AndrewLangvt]

Nice code changes @cimendes

Successful testing
TheiaCov_Clearlabs: https://app.terra.bio/#workspaces/theiagen-training-workspaces/Theiagen_Lang_Sandbox/job_history/1559a325-a7a6-4728-9300-83cb1d2c3b47
TheiaCov_ONT: https://app.terra.bio/#workspaces/theiagen-training-workspaces/Theiagen_Lang_Sandbox/job_history/d4a554a3-0d85-41d5-b115-774b96b20661