setting vadr_skip_length via organism_parameters subworkflow as this …

[kapsakcj]

…is taxa-specific. not tested yet

This PR closes #.

🗑️ 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/No

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 : Yes/No

:clipboard: Workflow/Task Step Changes

🔄 Data Processing

Docker/software or software versions changed:

Databases or database versions changed:

Data processing/commands changed:

File processing changed:

Compute resources changed:

➡️ Inputs

⬅️ Outputs

:test_tube: Testing

Test Dataset

Commandline Testing with MiniWDL or Cromwell (optional)

Terra Testing

Suggested Scenarios for Reviewer to Test

Theiagen Version Release Testing (optional)

: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

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

Running a test of theiacov_illumina_PE here on a number of different organisms to see if vadr_skip_length input parameter set via organism_parameter subwf is functional or not: https://app.terra.bio/#workspaces/theiagen-validations/PHB_Validation_nextcladeV3testing/job_history/6abe6969-bfd9-44af-bd00-e780a9b66efe

[kapsakcj]

theiacov_ont test here (flu, SC2, MPox): https://app.terra.bio/#workspaces/theiagen-validations/PHB_Validation_nextcladeV3testing/job_history/93a0dcb3-65f6-4ee4-ad18-067df4394ef0

[kapsakcj]

will mark ready for review when my test workflows pass