Adding back the vadr_num_alerts string output to theiacov_fasta workflow. It appears that this output was accidentally removed in PR #194 and went unnoticed until we ran the TheiaValidate workflow for the 1.3.0 release.
This PR closes #306
🗑️ 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 : 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 : No
:clipboard: Workflow/Task Step Changes
🔄 Data Processing
Nothing has changed, we are just re-adding an output column to the workflow
Docker/software or software versions changed: N/A
Databases or database versions changed: N/A
Data processing/commands changed: N/A
File processing changed: N/A
Compute resources changed: N/A
➡️ Inputs
N/A
⬅️ Outputs
String? vadr_num_alerts = vadr.num_alerts added to theiacov_fasta WDL wf file
:test_tube: Testing
Test Dataset
re-tested in Terra using TheiaCov_FASTA validation dataset (includes SC2, Mpox, Flu)
Commandline Testing with MiniWDL or Cromwell (optional)
Testing just done in Terra, no local testing necessary
-Will changes require functional or validation testing (checking outputs etc) during the release? Yes, validation testing
-Do new samples need to be added to validation datasets? If so, upload these to the appropriate validation workspace Google bucket (). Please describe the new samples here and why these have been chosen. No
-Are there any output files that should be checked after running the version release testing? No
:microscope: Final Developer Checklist
[x] The workflow/task has been tested locally and results, including file contents, are as anticipated
[ ] 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)
Adding back the
vadr_num_alertsstring output to theiacov_fasta workflow. It appears that this output was accidentally removed in PR #194 and went unnoticed until we ran the TheiaValidate workflow for the 1.3.0 release.This PR closes #306
🗑️ 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 : 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 : No
:clipboard: Workflow/Task Step Changes
🔄 Data Processing
Nothing has changed, we are just re-adding an output column to the workflow
Docker/software or software versions changed: N/A
Databases or database versions changed: N/A
Data processing/commands changed: N/A
File processing changed: N/A
Compute resources changed: N/A
➡️ Inputs
N/A
⬅️ Outputs
String? vadr_num_alerts = vadr.num_alertsadded to theiacov_fasta WDL wf file:test_tube: Testing
Test Dataset
re-tested in Terra using TheiaCov_FASTA validation dataset (includes SC2, Mpox, Flu)
Commandline Testing with MiniWDL or Cromwell (optional)
Testing just done in Terra, no local testing necessary
Terra Testing
https://app.terra.bio/#workspaces/theiagen-validations/PHB_Validation_v1-3-0/job_history/1098810f-408d-42d3-8e20-23ce5530f5eb
Suggested Scenarios for Reviewer to Test
run anything through theiacov_fasta
Theiagen Version Release Testing (optional)
-Will changes require functional or validation testing (checking outputs etc) during the release? Yes, validation testing -Do new samples need to be added to validation datasets? If so, upload these to the appropriate validation workspace Google bucket (). Please describe the new samples here and why these have been chosen. No -Are there any output files that should be checked after running the version release testing? No
:microscope: Final Developer Checklist
🎯 Reviewer Checklist
🗂️ Associated Documentation (to be completed by Theiagen developer)