SonarQube Server does not analyze Git submodules in Pull Requests

[khaoula-c]

Context

In our GitHub Actions CI pipeline, the SonarQube server does not detect or analyze Git submodules during Pull Request analysis.

Branch analysis works as expected, but submodules are completely ignored by the SonarQube server when the analysis is triggered from a PR.

Environment

CI: GitHub Actions

SonarQube (Gradle)

JDK: 21 (Temurin)

Build tool: Gradle

Repository contains multiple Git submodules
Current configuration

sonar:
   name: Sonar Analysis
   runs-on: 
     group: test-deploy
   needs: [build, test]
   steps:
     - name: 'Checkout Repository'
       uses: actions/checkout@v6
       with:
         submodules: recursive
         token: ${{ env.GITHUB_TOKEN }}
         fetch-depth: 0
         
     - name: Setup Java 21
       uses: actions/setup-java@v5
       with:
         distribution: 'temurin'
         java-version: '21'
         cache: gradle
         
     - name: 'Download Jacoco Report'
       uses: actions/download-artifact@v5
       with:
          name: jacoco-report   
        
             
     - name: Setup Gradle
       uses: gradle/actions/setup-gradle@f29f5a9d7b09a7c6b29859002d29d24e1674c884

     - name:  'Report Code coverage and quality'
       run: ./gradlew -xtest build jacocoTestReport sonar 
       env:
         JAVA_OPTS: "-Dfile.encoding=UTF-8 -Dsonar.projectKey=${{ secrets.SONAR_PROJECTKEY }} -Dsonar.coverage.jacoco.xmlReportPaths=jacocoTestReport.xml -Dsonar.log.level=INFO "

Observed behavior

Submodules are correctly cloned locally during the CI job.

SonarQube analysis on Pull Requests ignores the submodule code.

The issue does not occur on branch analysis (only on PRs)