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feat(wes): add CLI support #51

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9 tasks
Tracked by #48
pavelnikonorov opened this issue Oct 31, 2024 · 0 comments
Open
9 tasks
Tracked by #48

feat(wes): add CLI support #51

pavelnikonorov opened this issue Oct 31, 2024 · 0 comments

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@pavelnikonorov
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pavelnikonorov commented Oct 31, 2024

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.

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