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Fix CI workflow YAML parse error in artifact upload step#18

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ypriverol merged 1 commit intofeature/dat-bypass-workflowfrom
copilot/fix-ci-yml-workflow
Apr 13, 2026
Merged

Fix CI workflow YAML parse error in artifact upload step#18
ypriverol merged 1 commit intofeature/dat-bypass-workflowfrom
copilot/fix-ci-yml-workflow

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Copilot AI commented Apr 13, 2026

The CI workflow file had malformed YAML in the final artifact upload step, causing workflow parsing to fail before jobs could run. This update corrects the structure of that block.

  • Workflow YAML correction

    • Fixed indentation in .github/workflows/ci.yml for the Upload nextflow log step so with inputs are valid mappings.
    • No behavior changes to job logic, triggers, or step ordering.
  • Updated block

    - uses: actions/upload-artifact@v4
      if: always()
      name: Upload nextflow log
      with:
        name: nextflow_log_${{ matrix.NXF_VER }}_${{ github.run_id }}
        include-hidden-files: true
        path: .nextflow.log
        if-no-files-found: warn

Agent-Logs-Url: https://github.com/bigbio/spectrafuse/sessions/955c5f4a-8a76-437f-b5c2-f9c5f8ba6f3d

Co-authored-by: ypriverol <52113+ypriverol@users.noreply.github.com>
@ypriverol ypriverol marked this pull request as ready for review April 13, 2026 21:03
@ypriverol ypriverol merged commit cccc8ac into feature/dat-bypass-workflow Apr 13, 2026
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Up to standards ✅

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