Allow for GT to be a nocall if GQ and PL[0] are zero instead of homre… #305
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| # For most projects, this workflow file will not need changing; you simply need | |
| # to commit it to your repository. | |
| # | |
| # You may wish to alter this file to override the set of languages analyzed, | |
| # or to provide custom queries or build logic. | |
| # | |
| # ******** NOTE ******** | |
| # We have attempted to detect the languages in your repository. Please check | |
| # the `language` matrix defined below to confirm you have the correct set of | |
| # supported CodeQL languages. | |
| # | |
| name: "CodeQL" | |
| on: | |
| push: | |
| branches: [ master, develop ] | |
| paths: | |
| - '**/CMakeLists.txt' | |
| - 'pom.xml' | |
| - 'src/main/**' | |
| - 'src/resources/**' | |
| - '.github/resources/codeql-config.yml' | |
| - '.github/workflows/codeql.yml' | |
| pull_request: | |
| branches: [ master, develop ] | |
| paths: | |
| - '**/CMakeLists.txt' | |
| - 'pom.xml' | |
| - 'src/main/**' | |
| - 'src/resources/**' | |
| - '.github/resources/codeql-config.yml' | |
| - '.github/workflows/codeql.yml' | |
| env: | |
| PREREQS_ENV: ${{github.workspace}}/prereqs.sh | |
| PREREQS_INSTALL_DIR: ${{github.workspace}}/prereqs | |
| CMAKE_INSTALL_PREFIX: ${{github.workspace}}/install | |
| GENOMICSDB_BUILD_DIR: ${{github.workspace}}/build | |
| jobs: | |
| analyze: | |
| name: Analyze | |
| runs-on: ubuntu-20.04 | |
| permissions: | |
| actions: read | |
| contents: read | |
| security-events: write | |
| strategy: | |
| fail-fast: false | |
| # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ] | |
| # Learn more about CodeQL language support at https://git.io/codeql-language-support | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-java@v3 | |
| with: | |
| distribution: 'temurin' | |
| java-package: jdk | |
| java-version: '17' | |
| # Initializes the CodeQL tools for scanning. | |
| - name: Initialize CodeQL | |
| uses: github/codeql-action/init@v2 | |
| with: | |
| config-file: ./.github/resources/codeql-config.yml | |
| languages: cpp, java | |
| # If you wish to specify custom queries, you can do so here or in a config file. | |
| # By default, queries listed here will override any specified in a config file. | |
| # Prefix the list here with "+" to use these queries and those in the config file. | |
| # queries: ./path/to/local/query, your-org/your-repo/queries@main | |
| - name: Cache built prerequisites for ubuntu | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ${{env.PREREQS_INSTALL_DIR}} | |
| ~/.m2/repository | |
| ~/awssdk-install | |
| ~/gcssdk-install | |
| ~/protobuf-install | |
| key: ubuntu-codeql-cache-prereqs-v1 | |
| - name: Build GenomicsDB | |
| shell: bash | |
| run: | | |
| $GITHUB_WORKSPACE/.github/scripts/cleanup_hosts.sh | |
| echo "Install Prerequisites for Linux.." | |
| pushd $GITHUB_WORKSPACE/scripts/prereqs | |
| sudo INSTALL_PREFIX=$PREREQS_INSTALL_DIR PREREQS_ENV=$PREREQS_ENV ./install_prereqs.sh | |
| popd | |
| echo "Install prerequisites for Linux DONE" | |
| source $PREREQS_ENV | |
| cmake $GITHUB_WORKSPACE -DCMAKE_PREFIX_PATH=$PREREQS_INSTALL_DIR -DBUILD_JAVA=1 -DCMAKE_INSTALL_PREFIX=$CMAKE_INSTALL_PREFIX | |
| make -j4 | |
| make install | |
| rm -fr dependencies/ src/test/ test/ | |
| # Autobuild attempts to build any compiled languages (C/C++, C#, or Java). | |
| # If this step fails, then you should remove it and run the build manually (see below) | |
| # - name: Autobuild | |
| # uses: github/codeql-action/autobuild@v1 | |
| - name: Perform CodeQL Analysis | |
| uses: github/codeql-action/analyze@v2 |