Add VADR to flu and RSV TheiaCoV

[cimendes]

This PR closes #295

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

:brain: Aim, Context and Functionality

This PR adds VADR to two new organisms:

• Flu
• RSV

Due to the limitations of the RSV model the VADR memory parameter has been exposed in the organisms parameter sub-workflow.

Additionally, the VADR container has been upgraded to the latest version: us-docker.pkg.dev/general-theiagen/staphb/vadr:1.6.3

:hammer_and_wrench: Impacted Workflows/Tasks & Changes Being Made

This will affect the behavior of the workflow(s) even if users don’t change any workflow inputs relative to the last version : Yes (Docker container has been updated)

Running this workflow on different occasions could result in different results, e.g. due to use of a live database, "latest" docker image, or stochastic data processing : No

:clipboard: Workflow/Task Step Changes

🔄 Data Processing

Docker/software or software versions changed: Yes, changed to us-docker.pkg.dev/general-theiagen/staphb/vadr:1.6.3

Databases or database versions changed: N/A

Data processing/commands changed: N/A

File processing changed: N/A

Compute resources changed: Memory for VADR has been adjusted depending on the organism (8 for all organisms except for RSV-A and RSV-B which is set to 32)

➡️ Inputs

None have been changed

⬅️ Outputs

None has been changed

:test_tube: Testing

Test Dataset

Commandline Testing with MiniWDL or Cromwell (optional)

Terra Testing

Flu

• TheiaCoV Illumina PE
• TheiaCoV ONT
• TheiaCoV FASTA

RSV

• TheiaCoV Illumina PE

Suggested Scenarios for Reviewer to Test

• The container for VADR has been updated to the latest version so it's important to test all the organisms that are called to ensure that no major unintended changes occurred:
  • mpxv
  • sc2
  • wnv

Theiagen Version Release Testing (optional)

:microscope: Final Developer Checklist

• [ ] The workflow/task has been tested locally and results, including file contents, are as anticipated
• [x] The workflow/task has been tested on Terra and results, including file contents, are as anticipated
• [x] The CI/CD has been adjusted and tests are passing (to be completed by Theiagen developer)
• [x] Code changes follow the style guide

🎯 Reviewer Checklist

• [x] All impacted workflows/tasks have been tested on Terra with a different dataset than used for development
• [x] All reviewer-suggested scenarios have been tested and any additional
• [x] All changed results have been confirmed to be accurate
• [x] All workflows/tasks impacted by change/s have been tested using a standard validation dataset to ensure no unintended change of functionality
• [x] All code adheres to the style guide
• [x] MD5 sums have been updated
• [x] The PR author has addressed all comments

🗂️ Associated Documentation (to be completed by Theiagen developer)

• [ ] Relevant documentation on the Public Health Resources "PHB Main" has been updated
• [ ] Workflow diagrams have been updated to reflect changes

[kapsakcj]

Nice work on this! I need some more time looking at this, but so far I've looked at your VADR on Flu tests on TheiaCoV_Illumina_PE

Thoughts so far:

• VADR on Flu is running appropriately. I was cross referencing the VADR on Flu tutorial and everything looks as expected.
  • Only 2 specific alerts: extrant5,extrant3 will cause failure, but everything else is just a warning. So perhaps we communicate that to users that you should submit your sequences to NCBI as long as there are no outright failures (even if there are >0 warnings)
• code changes look great so far. TY for adding & exposing vadr_memory. CI is passing. So far I don't have any requested changes.

Curtis TODO:

• [x] review VADR on RSV outputs
• [x] run SC2 samples through dev branch (ILMN PE wf) and ensure results are identical to using previous docker image with v1.4.2
• [x] run Mpox samples through dev branch (FASTA wf)
• [x] run WNV samples through dev branch (ILMN PE wf)

[kapsakcj]

Hmmmm I think we should enable the theiacov_Illumina_pe and se workflows in the CI for miniwdl and ensure they are updated. If we don't we're going to have CI failures after merging.

Similar to changes I've made in https://github.com/theiagen/public_health_bioinformatics/pull/375/files

I'm happy to do this, but let me know if for some reason you think that is a bad idea.

EDIT: I updated the CI, see below commits.

[kapsakcj]

VADR on RSV appears to be running appropriately as well. There were a few samples that passed w/ 0 VADR alerts and some that failed with 2 VADR alerts (SRR19134713)

Here are some tests I ran:

• ✅ TheiaCov_FASTA on Flu and RSV (both A and B) samples: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/7ebe1167-a4a9-47ef-8f19-c0685f8f4b15
• ✅ TheiaCoV_illumina_pe on RSV-A: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/68929b73-9e93-483f-b1b5-bc703b760d64
  • outputs look good, everything ran as expected
• ✅ TheiaCov_illumina_pe on sars-cov-2: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/344e5230-3c5b-4a5a-a2e2-b0f4809f8f89
  • outputs look good, everything ran as expected (yes, I expected lots of VADR alerts for these 2 samples)
• ✅ TheiaCov_Illumina_se on sars-cov-2: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/e2e8f477-55d0-4f6b-b089-b5e5fb337b91
  • outputs look good, everything ran as expected
• ✅ TheiaCoV_FASTA on MPXV: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/d2cd9cec-1b0e-48d6-928e-3a38063cb41f
  • outputs look good, everything ran as expected
• ✅ TheiaCoV_illumina_pe on WNV: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/7d55b9b2-ecbe-451f-9299-49f147284be4
  • outputs look good, everything ran as expected