The default was changed when working with monkeypox genomes, all clades and not just the outbreak clade IIb, where some crucial sequences in understanding the full evolutionary history of the pathogen were getting removed as outliers.
We are changing this back to the previous default of 4, which is perfect for SARS-CoV-2, but will advise users to change it accordingly depending on the pathogen, especially where genuine outliers (not sequencing or dating artefacts) are expected.
:clipboard: Workflow/Task Steps
Inputs
Outputs
Impacted Outputs
:test_tube: Testing
Locally
Terra
Scenarios for Reviewer to Test
:microscope: Quality checks
Pull Request (PR) checklist:
[X] Include a description of what is in this pull request in this message.
[X] The workflow/task has been tested locally and on Terra
[X] The CI/CD has been adjusted and tests are passing
Closes #249
:hammer_and_wrench: Changes Being Made
Reverted the augur refine input
clock_filter_iqdto previous default value of 4.Impacted Workflows/Tasks
task_augur_refine.wdl
:brain: Context and Rationale
The default was changed when working with monkeypox genomes, all clades and not just the outbreak clade IIb, where some crucial sequences in understanding the full evolutionary history of the pathogen were getting removed as outliers.
We are changing this back to the previous default of 4, which is perfect for SARS-CoV-2, but will advise users to change it accordingly depending on the pathogen, especially where genuine outliers (not sequencing or dating artefacts) are expected.
:clipboard: Workflow/Task Steps
Inputs
Outputs
Impacted Outputs
:test_tube: Testing
Locally
Terra
Scenarios for Reviewer to Test
:microscope: Quality checks
Pull Request (PR) checklist: