nf-core AWS full size tests #14
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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/atacseq' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| aligner: ["bwa", "bowtie2", "chromap", "star"] | |
| 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/atacseq/work-${{ github.sha }} | |
| parameters: | | |
| { | |
| "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", | |
| "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/atacseq/results-${{ github.sha }}", | |
| "aligner": "${{ matrix.aligner }}" | |
| } | |
| profiles: test_full | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: Seqera Platform debug log file | |
| path: | | |
| seqera_platform_action_*.log | |
| seqera_platform_action_*.json |