🗑️ This dev branch should be deleted after merging to main.
:brain: Aim, Context and Functionality
This PR adds the Freyja coverage value to the Terra data table as a workflow output to provide more QC metrics to users.
: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 New output will be provided as default
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 : Not that I'm aware of- no changes made could lead to variable results
New output, "freyja_coverage", containing coverage identified by Freyja and parsed from freyja_demixed.tsv file.
:clipboard: Workflow/Task Step Changes
🔄 Data Processing
Data is not processed differently. Coverage is now parsed to the data table only.
Docker/software or software versions changed: None
Databases or database versions changed: None
Data processing/commands changed: None
File processing changed: Coverage parsed from freyja_demixed.tsv file.
Compute resources changed: None
➡️ Inputs
No inputs have been changed
⬅️ Outputs
Freyja_coverage output has been added, parsing the coverage from the freyja_demixed.tsv file.
:test_tube: Testing
Test Dataset
Samples 427190 and 427194 from validations dataset
Commandline Testing with MiniWDL or Cromwell (optional)
Task was tested and completed successfully, outputting coverage value.
Validation testing required (unsure)
No samples need to be added to the validation dataset
No additional output files need to be changed owing to this PR
: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] 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)
[x] Relevant documentation on the Public Health Resources "PHB Main" has been updated
Docs have not been updated owing to retrospective docs update process for v1.3.0!
[x] Workflow diagrams have been updated to reflect changes
Not necessary!
This PR closes #287
🗑️ This dev branch should be deleted after merging to main.
:brain: Aim, Context and Functionality
This PR adds the Freyja coverage value to the Terra data table as a workflow output to provide more QC metrics to users.
: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 New output will be provided as default
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 : Not that I'm aware of- no changes made could lead to variable results
:clipboard: Workflow/Task Step Changes
🔄 Data Processing
Data is not processed differently. Coverage is now parsed to the data table only.
Docker/software or software versions changed: None
Databases or database versions changed: None
Data processing/commands changed: None
File processing changed: Coverage parsed from freyja_demixed.tsv file.
Compute resources changed: None
➡️ Inputs
No inputs have been changed
⬅️ Outputs
Freyja_coverageoutput has been added, parsing the coverage from the freyja_demixed.tsv file.:test_tube: Testing
Test Dataset
Samples 427190 and 427194 from validations dataset
Commandline Testing with MiniWDL or Cromwell (optional)
Task was tested and completed successfully, outputting coverage value.
Terra Testing
Workflow was tested on Terra, completed successfully and output was present in Terra data table. Job History: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Doughty_Sandbox/job_history/8ce04ed1-9c58-41c8-8996-11928b0b3a99
Suggested Scenarios for Reviewer to Test
Test functionality and output presence
Theiagen Version Release Testing (optional)
Validation testing required (unsure) No samples need to be added to the validation dataset No additional output files need to be changed owing to this PR
:microscope: Final Developer Checklist
🎯 Reviewer Checklist
🗂️ Associated Documentation (to be completed by Theiagen developer)