diff --git a/.github/workflows/build-test-rust-fakeminimap2.yaml b/.github/workflows/build-test-rust-fakeminimap2.yaml
index 64dfac5..70d15ae 100644
--- a/.github/workflows/build-test-rust-fakeminimap2.yaml
+++ b/.github/workflows/build-test-rust-fakeminimap2.yaml
@@ -13,7 +13,7 @@ jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         submodules: 'recursive'
     - run: cd fakeminimap2
@@ -24,7 +24,7 @@ jobs:
   test-macos:
     runs-on: macos-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         submodules: 'recursive'
     - run: cd fakeminimap2
diff --git a/.github/workflows/build-test-rust-minimap2-sys.yml b/.github/workflows/build-test-rust-minimap2-sys.yml
index e2890c6..0d19878 100644
--- a/.github/workflows/build-test-rust-minimap2-sys.yml
+++ b/.github/workflows/build-test-rust-minimap2-sys.yml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     container: messense/rust-musl-cross:x86_64-musl
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         submodules: 'recursive'
     - run: cd minimap2-sys
@@ -28,7 +28,7 @@ jobs:
   test-ubuntu:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         submodules: 'recursive'
     - run: cd minimap2-sys
@@ -40,7 +40,7 @@ jobs:
   test-android:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         submodules: 'recursive'
     - name: Install Rust Cross
@@ -55,7 +55,7 @@ jobs:
   test-macos-13:
     runs-on: macos-13
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         submodules: 'recursive'
     - run: cd minimap2-sys
@@ -67,7 +67,7 @@ jobs:
   test-macos-14:
     runs-on: macos-14
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         submodules: 'recursive'
     - run: cd minimap2-sys
@@ -79,7 +79,7 @@ jobs:
   test-macos-15:
     runs-on: macos-15
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         submodules: 'recursive'
     - run: cd minimap2-sys
diff --git a/.github/workflows/build-test-rust-minimap2.yaml b/.github/workflows/build-test-rust-minimap2.yaml
index 3c3baf1..372613b 100644
--- a/.github/workflows/build-test-rust-minimap2.yaml
+++ b/.github/workflows/build-test-rust-minimap2.yaml
@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     container: messense/rust-musl-cross:x86_64-musl
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         submodules: 'recursive'
     - name: Build
@@ -29,7 +29,7 @@ jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         submodules: 'recursive'
     - name: Build
@@ -44,7 +44,7 @@ jobs:
   test-macos:
     runs-on: macos-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         submodules: 'recursive'
     - name: Build
@@ -59,7 +59,7 @@ jobs:
   test-android:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         submodules: 'recursive'
     - name: Install Rust Cross
diff --git a/.github/workflows/build-test-rust-minimappers2.yaml b/.github/workflows/build-test-rust-minimappers2.yaml
index 2598eb9..381d6b2 100644
--- a/.github/workflows/build-test-rust-minimappers2.yaml
+++ b/.github/workflows/build-test-rust-minimappers2.yaml
@@ -34,7 +34,7 @@ jobs:
         python-version: ['3.9', '3.12', '3.13']
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         submodules: 'recursive'
     - name: Set up Python
diff --git a/.github/workflows/create-python-release.yaml b/.github/workflows/create-python-release.yaml
index 14787e7..c8b1a61 100644
--- a/.github/workflows/create-python-release.yaml
+++ b/.github/workflows/create-python-release.yaml
@@ -36,7 +36,7 @@ jobs:
             target: aarch64
     steps:
       - run: sudo apt-get update && sudo apt-get install -y build-essential
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           submodules: 'recursive'
       - run: cd minimappers2
@@ -101,7 +101,7 @@ jobs:
             target: aarch64
     steps:
       - run: sudo apt-get update && sudo apt-get install -y build-essential musl-tools
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           submodules: 'recursive'
       - run: cd minimappers2
@@ -142,7 +142,7 @@ jobs:
           - runner: macos-14
             target: aarch64
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           submodules: 'recursive'
       - run: cd minimappers2
diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml
index 4d9230d..3ab9255 100644
--- a/.github/workflows/draft-pdf.yml
+++ b/.github/workflows/draft-pdf.yml
@@ -11,7 +11,7 @@ jobs:
     name: Paper Draft
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Build draft PDF
         uses: openjournals/openjournals-draft-action@master
         with: