[Augur_PHB] Update ncov repo commit and remove reference input to augur clades task

[sage-wright]

This PR closes #234!

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

:brain: Aim, Context and Functionality

: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

• The ncov repo commit change will cause all future SARS-CoV-2 Augur trees to be built with updated lineages and clades as of 2024-02-01.

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:

Databases or database versions changed:

in the set_sc2_defaults task, the nextstrain_ncov_repo_commit was updated from "23d1243127e8838a61b7e5c1a72bc419bf8c5a0d" to "cec4fa0ecd8612e4363d40662060a5a9c712d67e" which differ in about 11 months of age.

Data processing/commands changed:

In task_augur_clades.wdl, the augur_clades task had previously used the --references "{reference_fasta}" input, but this was not implemented in the augur clades command, leading to a warning.

File processing changed:

Compute resources changed:

➡️ Inputs

The optional input nextstrain_ncov_repo_commit was updated to "cec4fa0ecd8612e4363d40662060a5a9c712d67e" and will affect all users if the input is left blank.

⬅️ Outputs

The clades_tsv file will now contain clades (intermediate file, not sent to Terra table), and the auspice_input_json file will now be able to be colored by clade.

:test_tube: Testing

Test Dataset

We tested on 7 SARS-CoV-2 Omicron samples from different Omicron clades.

Command-line Testing with MiniWDL or Cromwell (optional)

Command-line testing did not occur.

Terra Testing

This job demonstrates the correct output behavior from augur clades.

Suggested Scenarios for Reviewer to Test

More SC2 samples. Additionally, flu and mpox should be tested as well.

Theiagen Version Release Testing (optional)

In the release, this PR will require:

• validation testing (visual check)
• no new samples
• The auspice_input_json should be checked and compared with previous versions.

:microscope: Final Developer Checklist

• [x] 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
• [x] Workflow diagrams have been updated to reflect changes

[kapsakcj]

Reminder to myself: notify one laboratory (PR) that might be using this when PR is merged & dev branch is deleted

[jrotieno]

@sage-wright getting an error:

Error updating config
Failed to process workflow definition 'augur' (reason 1 of 1): Failed to process 'call clades_task.augur_clades' (reason 1 of 1): The call supplied a value 'reference_fasta' that doesn't exist in the task (or sub-workflow)

This has to do with the reference_fasta input commented out in the clades_task. Should that be reverted back?

[sage-wright]

No, it shouldn't be reverted since it was not used. We should remove the reference in the workflow.

[sage-wright]

@jrotieno, I fixed it!