nf-core cloud full size tests #78
Workflow file for this run
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| name: nf-core cloud 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 cloud | |
| on: | |
| release: | |
| types: [created] | |
| pull_request_review: | |
| types: [submitted] | |
| workflow_dispatch: | |
| inputs: | |
| test: | |
| description: "-profile test (smaller)" | |
| type: boolean | |
| default: true | |
| somatic: | |
| description: "Somatic full test" | |
| type: boolean | |
| default: false | |
| germline: | |
| description: "Germline full test" | |
| type: boolean | |
| default: false | |
| germline_ncbench_agilent: | |
| description: "Germline Agilent NCBench test" | |
| type: boolean | |
| default: false | |
| aws: | |
| description: "AWS Batch" | |
| type: boolean | |
| default: true | |
| azure: | |
| description: "Azure Batch" | |
| type: boolean | |
| default: true | |
| jobs: | |
| run-platform: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - profile: test_aws | |
| test: test | |
| cloud: aws | |
| compute_env: TOWER_COMPUTE_ENV | |
| workdir: TOWER_BUCKET_AWS | |
| - profile: test_azure | |
| test: test | |
| cloud: azure | |
| compute_env: TOWER_CE_AZURE_CPU | |
| workdir: TOWER_BUCKET_AZURE | |
| - profile: test_full_aws | |
| test: somatic | |
| cloud: aws | |
| compute_env: TOWER_COMPUTE_ENV | |
| workdir: TOWER_BUCKET_AWS | |
| - profile: test_full_azure | |
| test: somatic | |
| cloud: azure | |
| compute_env: TOWER_CE_AZURE_CPU | |
| workdir: TOWER_BUCKET_AZURE | |
| - profile: test_full_germline_aws | |
| test: germline | |
| cloud: aws | |
| compute_env: TOWER_COMPUTE_ENV | |
| workdir: TOWER_BUCKET_AWS | |
| - profile: test_full_germline_azure | |
| test: germline | |
| cloud: azure | |
| compute_env: TOWER_CE_AZURE_CPU | |
| workdir: TOWER_BUCKET_AZURE | |
| - profile: test_full_germline_ncbench_agilent | |
| test: germline_ncbench_agilent | |
| cloud: aws | |
| compute_env: TOWER_COMPUTE_ENV | |
| workdir: TOWER_BUCKET_AWS | |
| 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/sarek' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' | |
| runs-on: ubuntu-latest | |
| 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 $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required | |
| # Launch workflow on AWS Batch | |
| - name: Launch workflow via Seqera Platform | |
| uses: seqeralabs/action-tower-launch@v2 | |
| # If inputs item exists (i.e. workflow_dispatch), then we find matrix.test and check it is false | |
| # If is false, we negate and run the job | |
| if: ( !contains(inputs[matrix.test], 'false') && !contains(inputs[matrix.cloud], 'false') ) | |
| with: | |
| run_name: sarek_${{ matrix.profile }} | |
| workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} | |
| access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} | |
| compute_env: ${{ secrets[matrix.compute_env] }} | |
| revision: ${{ github.sha }} | |
| workdir: ${{ secrets[matrix.workdir] }}/work/sarek/work-${{ github.sha }}/${{ matrix.profile }} | |
| parameters: | | |
| { | |
| "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", | |
| "outdir": "${{ secrets[matrix.workdir] }}/sarek/results-${{ github.sha }}/${{ matrix.profile }}/" | |
| } | |
| profiles: ${{ matrix.profile }} | |
| - uses: actions/upload-artifact@v3 | |
| name: Save Logs | |
| if: success() || failure() | |
| with: | |
| name: tower-${{ matrix.profile }}-log | |
| path: | | |
| tower_action_*.log | |
| tower_action_*.json |