-
Notifications
You must be signed in to change notification settings - Fork 4
Open
Labels
language: ruststatus: blockedSomething prevents progressSomething prevents progresstopic: ga4gh-sdktype: code
Description
Add CLI commands leveraging the SDK WES client (#50) to support for the GA4GH Workflow Execution Service (WES) API, version 1.1.0.
This issue requires addressing the following tasks:
Implement the following commands in ./cli/src/main.rs:
- Submit a workflow to a WES instance:
ga4gh-cli wes create [workflow-file]
- List workflows:
ga4gh-cli wes list
Example output:
WORKFLOW ID NAME STATUS SUBMITTED DURATION OWNER
--------------------------------------------------------------------------------------------------------
abc123 RNAseq-pipeline RUNNING 2024-10-31 10:45 UTC 15m user1
def456 Variant-calling COMPLETED 2024-10-31 09:30 UTC 1h 12m user2
ghi789 QC-check FAILED 2024-10-31 08:00 UTC 23m user3
jkl012 Data-preprocessing CANCELED 2024-10-31 07:50 UTC 5m user4
mno345 Assembly QUEUED 2024-10-31 11:00 UTC - user1
- Check workflow status by its ID:
ga4gh-cli wes status [workflow-id]
- Cancel a workflow:
ga4gh-cli wes cancel [workflow-id]:
- Get metadata for a workflow:
ga4gh-cli wes metadata [workflow-id]:
- Retrieve workflow logs:
ga4gh-cli wes log [workflow-id]
- Fetch workflow outputs:
ga4gh-cli wes outputs [workflow-id]
- Add unit tests to ensure the reliability of the CLI WES Client.
- Update CLI documentation with examples for each WES method.
Additional context
- This issue is part of meta issue feat(wes): add support for the GA4GH WES API #48. Refer to it for context and additional information.
- This issue requires feat(wes): add SDK support #50 to be addressed first.
Reactions are currently unavailable
Metadata
Metadata
Assignees
Labels
language: ruststatus: blockedSomething prevents progressSomething prevents progresstopic: ga4gh-sdktype: code