update gpu snapshot (automated) #8
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| name: update-gpu-snapshot | |
| run-name: update gpu snapshot (automated) | |
| on: | |
| issue_comment: | |
| types: [created] | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver | |
| NFT_VER: "0.9.2" | |
| NXF_ANSI_LOG: false | |
| # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver | |
| NXF_VER: "24.10.5" | |
| jobs: | |
| update-gpu-snapshot: | |
| # Only run if comment is on a PR with the main repo, and if it contains the magic keywords | |
| if: > | |
| contains(github.event.comment.html_url, '/pull/') && | |
| contains(github.event.comment.body, '@nf-core-bot update gpu snapshot') && | |
| github.repository == 'nf-core/methylseq' | |
| runs-on: "runs-on=${{ github.run_id }}/family=g4dn.xlarge/image=ubuntu24-gpu-x64" | |
| steps: | |
| # indication that the snapshot is being updated | |
| - name: React on comment | |
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | |
| with: | |
| comment-id: ${{ github.event.comment.id }} | |
| reactions: eyes | |
| # Use the @nf-core-bot token to check out so we can push later | |
| - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| with: | |
| token: ${{ secrets.nf_core_bot_auth_token }} | |
| - name: Get the test path from the comment (after "@nf-core-bot update gpu snapshot path:") | |
| id: get-test-path | |
| run: | | |
| echo "test_path=$(echo ${{ github.event.comment.body }} | grep -oP 'path:\s*\K[^ ]+')" >> $GITHUB_OUTPUT | |
| - name: if test path is empty, exit | |
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | |
| if: steps.get-test-path.outputs.test_path == '' | |
| with: | |
| comment-id: ${{ github.event.comment.id }} | |
| reactions: "-1" | |
| - name: if test path is empty, exit | |
| if: steps.get-test-path.outputs.test_path == '' | |
| run: exit 0 | |
| # Action runs on the issue comment, so we don't get the PR by default | |
| # Use the gh cli to check out the PR | |
| - name: Checkout Pull Request | |
| run: gh pr checkout ${{ github.event.issue.number }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} | |
| - uses: actions/setup-java@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # v4 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ env.NXF_VER }}" | |
| - name: Set up Python | |
| uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 | |
| with: | |
| python-version: "3.13" | |
| - name: Set up nf-test | |
| uses: nf-core/setup-nf-test@v1 | |
| with: | |
| version: "${{ env.NFT_VER }}" | |
| install-pdiff: true | |
| - name: Test CUDA | |
| run: | | |
| nvidia-smi -L | |
| - name: Update gpu snapshot | |
| id: update-gpu-snapshot | |
| run: | | |
| nf-test test \ | |
| --profile=docker,gpu \ | |
| --verbose \ | |
| --ci \ | |
| --update-snapshot \ | |
| --filter pipeline,workflow \ | |
| --tag gpu \ | |
| ${{ steps.get-test-path.outputs.test_path }} | |
| - name: Commit & push changes | |
| run: | | |
| git config user.email "[email protected]" | |
| git config user.name "nf-core-bot" | |
| git config push.default upstream | |
| git add . | |
| git status | |
| git commit -m "[automated] Update GPU snapshot for ${{ steps.get-test-path.outputs.test_path }}" | |
| git push | |
| - name: React on comment (success) | |
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | |
| if: success() | |
| with: | |
| comment-id: ${{ github.event.comment.id }} | |
| reactions: hooray | |
| - name: React on comment (failure) | |
| uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | |
| if: failure() | |
| with: | |
| comment-id: ${{ github.event.comment.id }} | |
| reactions: confused |