update sentieon snapshot (automated) #384
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| name: update-sentieon-snapshot | |
| run-name: update sentieon snapshot (automated) | |
| on: | |
| issue_comment: | |
| types: [created] | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver | |
| NFT_VER: "0.9.3" | |
| NXF_ANSI_LOG: false | |
| # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver | |
| NXF_VER: "25.04.8" | |
| jobs: | |
| update-sentieon-snapshot: | |
| # Only run if comment is on a PR with the main repo, and if it contains the magic keywords | |
| if: > | |
| contains(github.event.comment.html_url, '/pull/') && | |
| contains(github.event.comment.body, '@nf-core-bot update sentieon snapshot') && | |
| github.repository == 'nf-core/modules' | |
| runs-on: | |
| - runs-on=${{ github.run_id }}-nf-test-changes | |
| - runner=4cpu-linux-x64 | |
| - image=ubuntu22-full-x64 | |
| steps: | |
| # indication that the snapshot is being updated | |
| - name: React on comment | |
| uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 | |
| 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@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 | |
| with: | |
| token: ${{ secrets.nf_core_bot_auth_token }} | |
| - name: Get the test path from the comment (after "@nf-core-bot update sentieon snapshot path:") | |
| id: get-test-path | |
| run: | | |
| echo "test_path=$(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@e8674b075228eee787fea43ef493e45ece1004c9 # v5 | |
| 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: ${{ secrets.nf_core_bot_auth_token }} | |
| - uses: actions/setup-java@dded0888837ed1f317902acf8a20df0ad188d165 # v5 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ env.NXF_VER }}" | |
| - name: Set up Python | |
| uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 | |
| with: | |
| python-version: "3.14" | |
| - name: Set up nf-test | |
| uses: nf-core/setup-nf-test@v1 | |
| with: | |
| version: "${{ env.NFT_VER }}" | |
| install-pdiff: true | |
| # Set up secrets | |
| - name: Set up Nextflow secrets | |
| env: | |
| SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} | |
| SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} | |
| if: env.SENTIEON_ENCRYPTION_KEY != '' && env.SENTIEON_LICENSE_MESSAGE != '' | |
| shell: bash | |
| run: | | |
| python -m pip install cryptography | |
| nextflow secrets set SENTIEON_AUTH_DATA $(python3 modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE") | |
| - name: Update sentieon snapshot | |
| id: update-sentieon-snapshot | |
| env: | |
| SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }} | |
| SENTIEON_AUTH_MECH: "GitHub Actions - token" | |
| run: | | |
| nf-test test \ | |
| --profile=docker \ | |
| --verbose \ | |
| --ci \ | |
| --update-snapshot \ | |
| --clean-snapshot \ | |
| --filter process,workflow \ | |
| --tag sentieon \ | |
| ${{ 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 sentieon snapshot" | |
| git push |