diff --git a/.github/workflows/integration-testing.yml b/.github/workflows/integration-testing.yml
index b805489eb..ca73f33ec 100644
--- a/.github/workflows/integration-testing.yml
+++ b/.github/workflows/integration-testing.yml
@@ -150,3 +150,297 @@ jobs:
     - uses: ./../action/analyze
       env:
         TEST_MODE: true
+  
+  runner-analyze-javascript-ubuntu:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Build runner
+      run: |
+        cd runner
+        npm install
+        npm run build-runner
+
+    - name: Run init
+      run: |
+        # Pass --config-file here, but not for other jobs in this workflow.
+        # This means we're testing the config file parsing in the runner
+        # but not slowing down all jobs unnecessarily as it doesn't add much
+        # testing the parsing on different operating systems and languages.
+        runner/dist/codeql-runner-linux init --repository $GITHUB_REPOSITORY --languages javascript --config-file ./.github/codeql/codeql-config.yml --github-url $GITHUB_SERVER_URL --github-auth ${{ github.token }}
+
+    - name: Run analyze
+      run: |
+        runner/dist/codeql-runner-linux analyze --repository $GITHUB_REPOSITORY --commit $GITHUB_SHA --ref $GITHUB_REF --github-url $GITHUB_SERVER_URL --github-auth ${{ github.token }}
+      env:
+        TEST_MODE: true
+  
+  runner-analyze-javascript-windows:
+    runs-on: windows-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Build runner
+      run: |
+        cd runner
+        npm install
+        npm run build-runner
+
+    - name: Run init
+      run: |
+        runner/dist/codeql-runner-win.exe init --repository $Env:GITHUB_REPOSITORY --languages javascript --github-url $Env:GITHUB_SERVER_URL --github-auth ${{ github.token }}
+
+    - name: Run analyze
+      run: |
+        runner/dist/codeql-runner-win.exe analyze --repository $Env:GITHUB_REPOSITORY --commit $Env:GITHUB_SHA --ref $Env:GITHUB_REF --github-url $Env:GITHUB_SERVER_URL --github-auth ${{ github.token }}
+      env:
+        TEST_MODE: true
+  
+  runner-analyze-javascript-macos:
+    runs-on: macos-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Build runner
+      run: |
+        cd runner
+        npm install
+        npm run build-runner
+
+    - name: Run init
+      run: |
+        runner/dist/codeql-runner-macos init --repository $GITHUB_REPOSITORY --languages javascript --config-file ./.github/codeql/codeql-config.yml --github-url $GITHUB_SERVER_URL --github-auth ${{ github.token }}
+
+    - name: Run analyze
+      run: |
+        runner/dist/codeql-runner-macos analyze --repository $GITHUB_REPOSITORY --commit $GITHUB_SHA --ref $GITHUB_REF --github-url $GITHUB_SERVER_URL --github-auth ${{ github.token }}
+      env:
+        TEST_MODE: true
+  
+  runner-analyze-csharp-ubuntu:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Move codeql-action
+      shell: bash
+      run: |
+        mkdir ../action
+        mv * .github ../action/
+        mv ../action/tests/multi-language-repo/{*,.github} .
+
+    - name: Build runner
+      run: |
+        cd ../action/runner
+        npm install
+        npm run build-runner
+
+    - name: Run init
+      run: |
+        ../action/runner/dist/codeql-runner-linux init --repository $GITHUB_REPOSITORY --languages csharp --github-url $GITHUB_SERVER_URL --github-auth ${{ github.token }}
+
+    - name: Build code
+      run: |
+        . ./codeql-runner/codeql-env.sh
+        dotnet build
+
+    - name: Run analyze
+      run: |
+        ../action/runner/dist/codeql-runner-linux analyze --repository $GITHUB_REPOSITORY --commit $GITHUB_SHA --ref $GITHUB_REF --github-url $GITHUB_SERVER_URL --github-auth ${{ github.token }}
+      env:
+        TEST_MODE: true
+  
+  runner-analyze-csharp-windows:
+    runs-on: windows-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Move codeql-action
+      shell: bash
+      run: |
+        mkdir ../action
+        mv * .github ../action/
+        mv ../action/tests/multi-language-repo/{*,.github} .
+
+    - name: Build runner
+      run: |
+        cd ../action/runner
+        npm install
+        npm run build-runner
+
+    - name: Run init
+      run: |
+        ../action/runner/dist/codeql-runner-win.exe init --repository $Env:GITHUB_REPOSITORY --languages csharp --github-url $Env:GITHUB_SERVER_URL --github-auth ${{ github.token }}
+
+    - name: Build code
+      shell: powershell
+      run: |
+        cat ./codeql-runner/codeql-env.sh | Invoke-Expression
+        dotnet build
+
+    - name: Run analyze
+      run: |
+        ../action/runner/dist/codeql-runner-win.exe analyze --repository $Env:GITHUB_REPOSITORY --commit $Env:GITHUB_SHA --ref $Env:GITHUB_REF --github-url $Env:GITHUB_SERVER_URL --github-auth ${{ github.token }}
+      env:
+        TEST_MODE: true
+
+  runner-analyze-csharp-macos:
+    runs-on: macos-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Move codeql-action
+      shell: bash
+      run: |
+        mkdir ../action
+        mv * .github ../action/
+        mv ../action/tests/multi-language-repo/{*,.github} .
+
+    - name: Build runner
+      run: |
+        cd ../action/runner
+        npm install
+        npm run build-runner
+
+    - name: Run init
+      run: |
+        ../action/runner/dist/codeql-runner-macos init --repository $GITHUB_REPOSITORY --languages csharp --github-url $GITHUB_SERVER_URL --github-auth ${{ github.token }}
+
+    - name: Build code
+      shell: bash
+      run: |
+        . ./codeql-runner/codeql-env.sh
+        dotnet build
+
+    - name: Run analyze
+      run: |
+        ../action/runner/dist/codeql-runner-macos analyze --repository $GITHUB_REPOSITORY --commit $GITHUB_SHA --ref $GITHUB_REF --github-url $GITHUB_SERVER_URL --github-auth ${{ github.token }}
+      env:
+        TEST_MODE: true
+
+  
+  runner-analyze-csharp-autobuild-ubuntu:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Move codeql-action
+      shell: bash
+      run: |
+        mkdir ../action
+        mv * .github ../action/
+        mv ../action/tests/multi-language-repo/{*,.github} .
+
+    - name: Build runner
+      run: |
+        cd ../action/runner
+        npm install
+        npm run build-runner
+
+    - name: Run init
+      run: |
+        ../action/runner/dist/codeql-runner-linux init --repository $GITHUB_REPOSITORY --languages csharp --github-url $GITHUB_SERVER_URL --github-auth ${{ github.token }}
+
+    - name: Build code
+      run: |
+        ../action/runner/dist/codeql-runner-linux autobuild
+
+    - name: Run analyze
+      run: |
+        ../action/runner/dist/codeql-runner-linux analyze --repository $GITHUB_REPOSITORY --commit $GITHUB_SHA --ref $GITHUB_REF --github-url $GITHUB_SERVER_URL --github-auth ${{ github.token }}
+      env:
+        TEST_MODE: true
+  
+  runner-analyze-csharp-autobuild-windows:
+    runs-on: windows-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Move codeql-action
+      shell: bash
+      run: |
+        mkdir ../action
+        mv * .github ../action/
+        mv ../action/tests/multi-language-repo/{*,.github} .
+
+    - name: Build runner
+      run: |
+        cd ../action/runner
+        npm install
+        npm run build-runner
+
+    - name: Run init
+      run: |
+        ../action/runner/dist/codeql-runner-win.exe init --repository $Env:GITHUB_REPOSITORY --languages csharp --github-url $Env:GITHUB_SERVER_URL --github-auth ${{ github.token }}
+
+    - name: Build code
+      shell: powershell
+      run: |
+        ../action/runner/dist/codeql-runner-win.exe autobuild
+
+    - name: Run analyze
+      run: |
+        ../action/runner/dist/codeql-runner-win.exe analyze --repository $Env:GITHUB_REPOSITORY --commit $Env:GITHUB_SHA --ref $Env:GITHUB_REF --github-url $Env:GITHUB_SERVER_URL --github-auth ${{ github.token }}
+      env:
+        TEST_MODE: true
+
+  runner-analyze-csharp-autobuild-macos:
+    runs-on: macos-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Move codeql-action
+      shell: bash
+      run: |
+        mkdir ../action
+        mv * .github ../action/
+        mv ../action/tests/multi-language-repo/{*,.github} .
+
+    - name: Build runner
+      run: |
+        cd ../action/runner
+        npm install
+        npm run build-runner
+
+    - name: Run init
+      run: |
+        ../action/runner/dist/codeql-runner-macos init --repository $GITHUB_REPOSITORY --languages csharp --github-url $GITHUB_SERVER_URL --github-auth ${{ github.token }}
+
+    - name: Build code
+      shell: bash
+      run: |
+        ../action/runner/dist/codeql-runner-macos autobuild
+
+    - name: Run analyze
+      run: |
+        ../action/runner/dist/codeql-runner-macos analyze --repository $GITHUB_REPOSITORY --commit $GITHUB_SHA --ref $GITHUB_REF --github-url $GITHUB_SERVER_URL --github-auth ${{ github.token }}
+      env:
+        TEST_MODE: true
+
+  runner-upload-sarif:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Build runner
+      run: |
+        cd runner
+        npm install
+        npm run build-runner
+
+    - name: Upload with runner
+      run: |
+        # Deliberately don't use TEST_MODE here. This is specifically testing
+        # the compatibility with the API.
+        runner/dist/codeql-runner-linux upload --sarif-file src/testdata/empty-sarif.sarif --repository $GITHUB_REPOSITORY --commit $GITHUB_SHA --ref $GITHUB_REF --github-url $GITHUB_SERVER_URL --github-auth ${{ github.token }}
diff --git a/.github/workflows/runner.yml b/.github/workflows/runner.yml
deleted file mode 100644
index 8e8f9f30b..000000000
--- a/.github/workflows/runner.yml
+++ /dev/null
@@ -1,26 +0,0 @@
-name: "CodeQL runner"
-
-on: [push, pull_request]
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v2
-
-    - name: Build runner
-      run: |
-        cd runner
-        npm install
-        npm run build-runner
-
-    - name: Upload with runner
-      run: |
-        runner/dist/codeql-runner-linux upload \
-          --sarif-file src/testdata/empty-sarif.sarif \
-          --repository $GITHUB_REPOSITORY \
-          --commit $GITHUB_SHA \
-          --ref $GITHUB_REF \
-          --github-url $GITHUB_SERVER_URL \
-          --github-auth ${{ github.token }}
diff --git a/lib/fingerprints.test.js b/lib/fingerprints.test.js
index e9203e538..51a536e38 100644
--- a/lib/fingerprints.test.js
+++ b/lib/fingerprints.test.js
@@ -95,6 +95,16 @@ ava_1.default('hash', (t) => {
         "cc97dc7b1d7d8f7b:1",
         "c129715d7a2bc9a3:1"
     ]);
+    testHash(t, "x = 2\nx = 1\nprint(x)\nx = 3\nprint(x)\nx = 4\nprint(x)\n", [
+        "e54938cc54b302f1:1",
+        "bb609acbe9138d60:1",
+        "1131fd5871777f34:1",
+        "5c482a0f8b35ea28:1",
+        "54517377da7028d2:1",
+        "2c644846cb18d53e:1",
+        "f1b89f20de0d133:1",
+        "c129715d7a2bc9a3:1"
+    ]);
 });
 function testResolveUriToFile(uri, index, artifactsURIs) {
     const location = { "uri": uri, "index": index };
diff --git a/lib/fingerprints.test.js.map b/lib/fingerprints.test.js.map
index 4581b299a..f0731dfbb 100644
--- a/lib/fingerprints.test.js.map
+++ b/lib/fingerprints.test.js.map
@@ -1 +1 @@
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\ No newline at end of file
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\ No newline at end of file
diff --git a/src/fingerprints.test.ts b/src/fingerprints.test.ts
index aee473ee1..fc4460a1d 100644
--- a/src/fingerprints.test.ts
+++ b/src/fingerprints.test.ts
@@ -111,6 +111,20 @@ test('hash', (t: ava.Assertions) => {
       "cc97dc7b1d7d8f7b:1",
       "c129715d7a2bc9a3:1"
     ]);
+
+  testHash(
+    t,
+    "x = 2\nx = 1\nprint(x)\nx = 3\nprint(x)\nx = 4\nprint(x)\n",
+    [
+      "e54938cc54b302f1:1",
+      "bb609acbe9138d60:1",
+      "1131fd5871777f34:1",
+      "5c482a0f8b35ea28:1",
+      "54517377da7028d2:1",
+      "2c644846cb18d53e:1",
+      "f1b89f20de0d133:1",
+      "c129715d7a2bc9a3:1"
+    ]);
 });
 
 function testResolveUriToFile(uri: any, index: any, artifactsURIs: any[]) {
diff --git a/tests/multi-language-repo/csharp.csproj b/tests/multi-language-repo/csharp.csproj
index 376c93ec8..438ab8a4d 100644
--- a/tests/multi-language-repo/csharp.csproj
+++ b/tests/multi-language-repo/csharp.csproj
@@ -4,6 +4,7 @@
     <OutputType>Exe</OutputType>
     <TargetFramework>netcoreapp3.1</TargetFramework>
     <RootNamespace>multi_language_test</RootNamespace>
+    <DefaultItemExcludes>$(DefaultItemExcludes);codeql-runner/**</DefaultItemExcludes>
   </PropertyGroup>
 
 </Project>