Closed kapsakcj closed 2 months ago
Managed to import this branch without issue on Terra (failed with version in main) for Pangolin_Update_PHB
Testing pango update here: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/7c2b9d62-1df0-40c6-b000-7fc649aeb1ad
✅ working like a charm!
This PR closes #.
🗑️ This dev branch should be deleted after merging to main.
:brain: Aim, Context and Functionality
Pangolin_Update workflow: We missed deleting the
nextclade_dataset_reference_input
from org param call block when updating to nextclade V3 in #375 . This caused an error in Terra since the workflow was non-functional and did not passminiwdl check
orwomtools validate
Additionally, for theiacov_ONT and TheiaCoV_Illumina_PE workflows: added
gene_locations_bed_file
to org param call blocks to hide optional input from user. This input should be hidden from the user in Terra because it will not be used even if a File is provided by the user.: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, these are just workflow level Input changes
Docker/software or software versions changed: No
Databases or database versions changed: No
Data processing/commands changed: No
File processing changed: No
Compute resources changed: No
➡️ Inputs
gene_locations_bed_file
to org param call blocks to hide optional input from usernextclade_dataset_reference_input
from org param call block for Pangolin_Update workflow⬅️ Outputs
N/A
:test_tube: Testing
Test Dataset
Pangolin_Update test: 4 sars-cov-2 samples
TheiaCoV_Illumina_PE and ONT: Not sure? Perhaps test with Flu samples through both?
Commandline Testing with MiniWDL or Cromwell (optional)
N/A
Terra Testing
workflow ran successfully:![image](https://github.com/theiagen/public_health_bioinformatics/assets/8172086/b1ab22a7-0b18-4548-aa62-b7983a0e4aa4)
⚠️ Just need to check that the workflows ran successfullyWorkflows ran successfully ✅⚠️ Just need to check that the workflows ran successfullyWorkflows ran successfully ✅For both of these workflows ⬆️ , the![image](https://github.com/theiagen/public_health_bioinformatics/assets/8172086/65e69ab7-384f-4f8b-93c2-a9f444ff5f9e)
gene_locations_bed_file
input has been hidden from the user, as expected:Suggested Scenarios for Reviewer to Test
For pangolin_update, any sars-cov-2 samples that have been previously run through Pangolin (via TheiaCoV workflows)
Likely test Flu samples through ILMN PE and ONT workflows
Theiagen Version Release Testing (optional)
:microscope: Final Developer Checklist
🎯 Reviewer Checklist
🗂️ Associated Documentation (to be completed by Theiagen developer)