diff --git a/.github/workflows/ci_cmake.yml b/.github/workflows/ci_cmake.yml
index 0bd5d86db2..fa785d276d 100644
--- a/.github/workflows/ci_cmake.yml
+++ b/.github/workflows/ci_cmake.yml
@@ -49,7 +49,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Configure tests
         run: |
diff --git a/.github/workflows/ci_coverage.yml b/.github/workflows/ci_coverage.yml
index 68be372528..1ab89f4ddd 100644
--- a/.github/workflows/ci_coverage.yml
+++ b/.github/workflows/ci_coverage.yml
@@ -38,7 +38,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
diff --git a/.github/workflows/ci_documentation.yml b/.github/workflows/ci_documentation.yml
index d9d1bfb224..ff2e9a1d08 100644
--- a/.github/workflows/ci_documentation.yml
+++ b/.github/workflows/ci_documentation.yml
@@ -34,12 +34,12 @@ jobs:
     steps:
       - name: Checkout
         if: github.event_name != 'pull_request_target'
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       # pull_request_target does not checkout the merge commit by default
       - name: Checkout
         if: github.event_name == 'pull_request_target'
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           ref: "refs/pull/${{ github.event.number }}/merge"
 
diff --git a/.github/workflows/ci_license.yml b/.github/workflows/ci_license.yml
index e155addcd4..9f420b0315 100644
--- a/.github/workflows/ci_license.yml
+++ b/.github/workflows/ci_license.yml
@@ -32,7 +32,7 @@ jobs:
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: REUSE Compliance Check
         uses: fsfe/reuse-action@v5
diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml
index e1fdba9b18..6e846c0507 100644
--- a/.github/workflows/ci_linux.yml
+++ b/.github/workflows/ci_linux.yml
@@ -38,7 +38,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Setup cache
         uses: seqan/actions/setup-actions-cache@main
diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml
index 751bbca1ba..bb2558a56b 100644
--- a/.github/workflows/ci_macos.yml
+++ b/.github/workflows/ci_macos.yml
@@ -36,7 +36,7 @@ jobs:
         compiler: ["clang-latest", "clang-second-latest", "clang-third-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest"]
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Setup toolchain
         uses: seqan/actions/setup-toolchain@main
diff --git a/.github/workflows/ci_misc.yml b/.github/workflows/ci_misc.yml
index 358498cc00..1a05ccb65b 100644
--- a/.github/workflows/ci_misc.yml
+++ b/.github/workflows/ci_misc.yml
@@ -39,7 +39,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Setup cache
         uses: seqan/actions/setup-actions-cache@main
diff --git a/.github/workflows/ci_update_cookbook.yml b/.github/workflows/ci_update_cookbook.yml
index ef8c7a55ec..532ee53046 100644
--- a/.github/workflows/ci_update_cookbook.yml
+++ b/.github/workflows/ci_update_cookbook.yml
@@ -28,7 +28,7 @@ jobs:
     timeout-minutes: 15
     steps:
       - name: Checkout SeqAn3
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           token: ${{ secrets.SEQAN_ACTIONS_PAT }}
 
diff --git a/.github/workflows/cron_api.yml b/.github/workflows/cron_api.yml
index 33594dc6a8..1a6302d89d 100644
--- a/.github/workflows/cron_api.yml
+++ b/.github/workflows/cron_api.yml
@@ -37,7 +37,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Configure tests
         run: |
diff --git a/.github/workflows/cron_avx2.yml b/.github/workflows/cron_avx2.yml
index 2a91d846cb..29e7c65b3f 100644
--- a/.github/workflows/cron_avx2.yml
+++ b/.github/workflows/cron_avx2.yml
@@ -39,7 +39,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Configure tests
         run: |
diff --git a/.github/workflows/cron_codeql.yml b/.github/workflows/cron_codeql.yml
index a962e2e8ab..1195efd74c 100644
--- a/.github/workflows/cron_codeql.yml
+++ b/.github/workflows/cron_codeql.yml
@@ -33,7 +33,7 @@ jobs:
       image: ghcr.io/seqan/gcc-second-latest
     steps:
     - name: Checkout
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
 
     - name: Initialize CodeQL
       uses: github/codeql-action/init@v3
diff --git a/.github/workflows/cron_latest_libraries.yml b/.github/workflows/cron_latest_libraries.yml
index 5a7ea156c9..ef66f45833 100644
--- a/.github/workflows/cron_latest_libraries.yml
+++ b/.github/workflows/cron_latest_libraries.yml
@@ -39,7 +39,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Update dependencies
         run: |
diff --git a/.github/workflows/cron_no_optional_libraries.yml b/.github/workflows/cron_no_optional_libraries.yml
index c8c031c50d..642d2a494e 100644
--- a/.github/workflows/cron_no_optional_libraries.yml
+++ b/.github/workflows/cron_no_optional_libraries.yml
@@ -53,7 +53,7 @@ jobs:
       image: ${{ matrix.image || '' }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Setup compiler
         if: contains(matrix.os, 'macos')
diff --git a/.github/workflows/cron_sanitizer.yml b/.github/workflows/cron_sanitizer.yml
index d06fd87725..6abdd5db9e 100644
--- a/.github/workflows/cron_sanitizer.yml
+++ b/.github/workflows/cron_sanitizer.yml
@@ -77,7 +77,7 @@ jobs:
       image: ${{ matrix.image || '' }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Setup compiler
         if: contains(matrix.os, 'macos')
diff --git a/.github/workflows/ram_usage.yml b/.github/workflows/ram_usage.yml
index 6a173c136b..db43c8eae2 100644
--- a/.github/workflows/ram_usage.yml
+++ b/.github/workflows/ram_usage.yml
@@ -35,7 +35,7 @@ jobs:
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
     steps:
       - name: Checkout SeqAn3
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           path: seqan3