nf-core AWS full size tests #23
Workflow file for this run
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| name: nf-core AWS full size tests | |
| # This workflow is triggered on PRs opened against the master branch. | |
| # It can be additionally triggered manually with GitHub actions workflow dispatch button. | |
| # It runs the -profile 'test_full' on AWS batch | |
| on: | |
| pull_request: | |
| branches: | |
| - master | |
| workflow_dispatch: | |
| pull_request_review: | |
| types: [submitted] | |
| jobs: | |
| run-platform: | |
| name: Run AWS full tests | |
| # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered | |
| if: github.repository == 'nf-core/viralrecon' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' | |
| runs-on: ubuntu-latest | |
| # Do a full-scale run with data from each sequencing platform | |
| strategy: | |
| matrix: | |
| platform: ["illumina", "nanopore"] | |
| steps: | |
| - uses: octokit/[email protected] | |
| id: check_approvals | |
| with: | |
| route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - id: test_variables | |
| if: github.event_name != 'workflow_dispatch' | |
| run: | | |
| JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' | |
| CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') | |
| test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required | |
| - name: Launch workflow via Seqera Platform | |
| uses: seqeralabs/action-tower-launch@v2 | |
| with: | |
| workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} | |
| access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} | |
| compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} | |
| revision: ${{ github.sha }} | |
| workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/viralrecon/work-${{ github.sha }} | |
| parameters: | | |
| { | |
| "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", | |
| "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/viralrecon/results-${{ github.sha }}/platform_${{ matrix.platform }}" | |
| } | |
| profiles: test_full_${{ matrix.platform }},aws_tower | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: Seqera Platform debug log file | |
| path: | | |
| seqera_platform_action_*.log | |
| seqera_platform_action_*.json |