nf-core AWS full size tests #416
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 main/master branch. | |
| # It can be additionally triggered manually with GitHub actions workflow dispatch button. | |
| # It runs the -profile 'test_full' on AWS batch | |
| on: | |
| workflow_dispatch: | |
| pull_request_review: | |
| types: [submitted] | |
| release: | |
| types: [published] | |
| jobs: | |
| run-platform: | |
| name: Run AWS full tests (${{ matrix.aligner }} - ${{ matrix.compute_env }}) | |
| # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered | |
| if: github.repository == 'nf-core/methylseq' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' || github.event_name == 'release' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| include: | |
| - aligner: "bismark" | |
| profile: "test_full" | |
| compute_env: "CPU" | |
| - aligner: "bismark_hisat" | |
| profile: "test_full" | |
| compute_env: "CPU" | |
| - aligner: "bwameth" | |
| profile: "test_full" | |
| compute_env: "CPU" | |
| - aligner: "bwameth" | |
| profile: "test_full,gpu" | |
| compute_env: "GPU" | |
| - aligner: "bismark" | |
| profile: "test_full" | |
| compute_env: "ARM" | |
| - aligner: "bismark_hisat" | |
| profile: "test_full" | |
| compute_env: "ARM" | |
| - aligner: "bwameth" | |
| profile: "test_full" | |
| compute_env: "ARM" | |
| steps: | |
| - name: Set revision variable | |
| id: revision | |
| run: | | |
| echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT" | |
| - name: Validate parameters | |
| run: | | |
| echo "Workspace ID: ${{ vars.TOWER_WORKSPACE_ID }}" | |
| echo "Compute Env: ${{ matrix.compute_env == 'CPU' && vars.TOWER_COMPUTE_ENV_CPU || matrix.compute_env == 'GPU' && vars.TOWER_COMPUTE_ENV_GPU || vars.TOWER_COMPUTE_ENV_ARM }}" | |
| echo "Access token present: ${{ secrets.TOWER_ACCESS_TOKEN != '' }}" | |
| - name: Launch workflow via Seqera Platform | |
| uses: seqeralabs/action-tower-launch@v2 | |
| with: | |
| workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} | |
| access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} | |
| compute_env: ${{ matrix.compute_env == 'CPU' && vars.TOWER_COMPUTE_ENV_CPU || matrix.compute_env == 'GPU' && vars.TOWER_COMPUTE_ENV_GPU || vars.TOWER_COMPUTE_ENV_ARM }} | |
| revision: ${{ steps.revision.outputs.revision }} | |
| workdir: s3://nf-core-awsmegatests/work/methylseq/work-${{ steps.revision.outputs.revision }}-${{ matrix.aligner }}-${{ matrix.compute_env }} | |
| labels: ${{ matrix.compute_env == 'GPU' && 'full_test,gpu' || matrix.compute_env == 'ARM' && 'full_test,arm,wave' || 'full_test' }} | |
| parameters: | | |
| { | |
| "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", | |
| "outdir": "s3://nf-core-awsmegatests/methylseq/results-${{ steps.revision.outputs.revision }}-${{ matrix.aligner }}-${{ matrix.compute_env }}", | |
| "aligner": "${{ matrix.aligner }}" | |
| } | |
| profiles: ${{ matrix.profile }} | |
| - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 | |
| with: | |
| name: Seqera Platform debug log file (${{ matrix.aligner }}-${{ matrix.compute_env }}) | |
| path: | | |
| seqera_platform_action_*.log | |
| seqera_platform_action_*.json |