21.04.1 List of changes done by Lifebit #61
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| name: Nextflow CI | |
| # This workflow is triggered on pushes to the repository. | |
| on: | |
| pull_request: | |
| branches: | |
| - '*' | |
| paths-ignore: | |
| - 'CHANGELOG.md' | |
| push: | |
| branches: | |
| - 'main' | |
| - v[0-9]+.[0-9]+.[0-9]+ | |
| paths-ignore: | |
| - '.github/**' | |
| - 'CHANGELOG.md' | |
| jobs: | |
| build: | |
| name: Build Nextflow | |
| if: "!contains(github.event.head_commit.message, '[ci skip]')" | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 90 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| java_version: [8, 11, 15] | |
| steps: | |
| - name: Environment | |
| run: env | sort | |
| - name: Checkout | |
| uses: actions/checkout@v1 | |
| with: | |
| fetch-depth: 1 | |
| submodules: true | |
| - name: Setup env | |
| run: | | |
| rm -f $HOME/.gitconfig; | |
| mkdir -p "$HOME/.nextflow"; | |
| echo "providers.github.auth='$NXF_GITHUB_ACCESS_TOKEN'" > "$HOME/.nextflow/scm" | |
| - name: Setup Java ${{ matrix.java_version }} | |
| uses: actions/setup-java@v1 | |
| with: | |
| java-version: ${{matrix.java_version}} | |
| architecture: x64 | |
| - name: Compile | |
| run: make assemble | |
| - name: Tests | |
| run: make test | |
| env: | |
| GRADLE_OPTS: '-Dorg.gradle.daemon=false' | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| NXF_BITBUCKET_ACCESS_TOKEN: ${{ secrets.NXF_BITBUCKET_ACCESS_TOKEN }} | |
| NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }} | |
| NXF_GITLAB_ACCESS_TOKEN: ${{ secrets.NXF_GITLAB_ACCESS_TOKEN }} | |
| NXF_AZURE_REPOS_TOKEN: ${{ secrets.NXF_AZURE_REPOS_TOKEN }} | |
| AZURE_STORAGE_ACCOUNT_NAME: nfbucket | |
| AZURE_STORAGE_ACCOUNT_KEY: ${{ secrets.AZURE_STORAGE_ACCOUNT_KEY }} | |
| AZURE_BATCH_ACCOUNT_KEY: ${{ secrets.AZURE_BATCH_ACCOUNT_KEY }} | |
| - name: Integration | |
| if: "!contains(github.event.head_commit.message, '[ci fast]')" | |
| run: make install && ./integration-tests.sh | |
| env: | |
| TEST_JDK: ${{ matrix.java_version }} | |
| GRADLE_OPTS: '-Dorg.gradle.daemon=false' | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| NXF_BITBUCKET_ACCESS_TOKEN: ${{ secrets.NXF_BITBUCKET_ACCESS_TOKEN }} | |
| NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }} | |
| NXF_GITLAB_ACCESS_TOKEN: ${{ secrets.NXF_GITLAB_ACCESS_TOKEN }} | |
| NXF_AZURE_REPOS_TOKEN: ${{ secrets.NXF_AZURE_REPOS_TOKEN }} | |
| TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }} | |
| GOOGLE_SECRET: ${{ secrets.GOOGLE_SECRET }} | |
| AZURE_STORAGE_ACCOUNT_NAME: nfbucket | |
| AZURE_STORAGE_ACCOUNT_KEY: ${{ secrets.AZURE_STORAGE_ACCOUNT_KEY }} | |
| AZURE_BATCH_ACCOUNT_KEY: ${{ secrets.AZURE_BATCH_ACCOUNT_KEY }} | |
| - name: Setup Java 8 | |
| if: "matrix.java_version != 8 && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/testing') && !contains(github.event.head_commit.message, '[ci fast]')" | |
| uses: actions/setup-java@v1 | |
| with: | |
| java-version: 8 | |
| architecture: x64 | |
| - name: Integration vs Java 8 | |
| if: "matrix.java_version != 8 && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/testing') && !contains(github.event.head_commit.message, '[ci fast]')" | |
| run: ./integration-tests.sh | |
| env: | |
| TEST_JDK: 8 | |
| TEST_SMOKE: true | |
| GRADLE_OPTS: '-Dorg.gradle.daemon=false' | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| NXF_BITBUCKET_ACCESS_TOKEN: ${{ secrets.NXF_BITBUCKET_ACCESS_TOKEN }} | |
| NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }} | |
| NXF_GITLAB_ACCESS_TOKEN: ${{ secrets.NXF_GITLAB_ACCESS_TOKEN }} | |
| NXF_AZURE_REPOS_TOKEN: ${{ secrets.NXF_AZURE_REPOS_TOKEN }} | |
| AZURE_STORAGE_ACCOUNT_NAME: nfbucket | |
| AZURE_STORAGE_ACCOUNT_KEY: ${{ secrets.AZURE_STORAGE_ACCOUNT_KEY }} | |
| AZURE_BATCH_ACCOUNT_KEY: ${{ secrets.AZURE_BATCH_ACCOUNT_KEY }} | |
| # - name: Publish | |
| # if: failure() | |
| # run: bash pub-tests.sh github | |
| # env: | |
| # TEST_JDK: ${{ matrix.java_version }} | |
| # NXF_AWS_ACCESS: ${{ secrets.NXF_AWS_ACCESS }} | |
| # NXF_AWS_SECRET: ${{ secrets.NXF_AWS_SECRET }} |