diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index e1cd040..32111e4 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -57,7 +57,7 @@ jobs:
     # are not available as wheels, pip will build a wheel for them, which can be cached.
     - name: Install wheel
       run: pip install wheel
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
       with:
         fetch-depth: 1
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -85,7 +85,7 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
       with:
         fetch-depth: 1
     - uses: actions/setup-python@v6
@@ -135,7 +135,7 @@ jobs:
     steps:
     # checkout the repository
     # and use it as the current working directory
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
       with:
         fetch-depth: 1
     - uses: actions/setup-python@v6
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 73fd0ed..b6cebb2 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -83,7 +83,7 @@ jobs:
         run: pip install wheel
       - name: Install flake8
         run: pip install flake8 flake8-import-order
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
       - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -116,7 +116,7 @@ jobs:
       matrix:
         python-version: ["3.11"]
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 1
       - uses: actions/setup-python@v6
@@ -160,7 +160,7 @@ jobs:
       matrix:
         python-version: ["3.11"]
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 1
       - uses: actions/setup-python@v6
@@ -192,7 +192,7 @@ jobs:
         os: [ubuntu-24.04]
         r-version: ["release"]
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 1
       - uses: r-lib/actions/setup-r@v2
@@ -227,7 +227,7 @@ jobs:
     if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
       - name: Check file sizes
@@ -270,7 +270,7 @@ jobs:
         ports:
           - 5432:5432
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 1
       - uses: actions/setup-python@v6
@@ -373,7 +373,7 @@ jobs:
       matrix:
         python-version: ["3.11"]
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 1
       - uses: actions/setup-python@v6
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index ab82ef5..65aafee 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -11,7 +11,7 @@ jobs:
     outputs:
       nb: ${{ steps.set-diff.outputs.nb }}
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -31,7 +31,7 @@ jobs:
       tag: ${{ steps.tag_label.outputs.tag }}
       changelog: ${{ steps.tag_raw.outputs.changelog }}
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -56,7 +56,7 @@ jobs:
     if: ${{ needs.Diff.outputs.nb > 0 }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -90,7 +90,7 @@ jobs:
     steps:
       # Get Data
       - name: 'Checkout'
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -124,7 +124,7 @@ jobs:
     if: ${{ needs.Diff.outputs.nb > 0 }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           persist-credentials: false
           fetch-depth: 0
diff --git a/.github/workflows/update.yml b/.github/workflows/update.yml
index dac6b97..7b93d65 100644
--- a/.github/workflows/update.yml
+++ b/.github/workflows/update.yml
@@ -15,7 +15,7 @@ jobs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
       - name: 'List repos'
         id: set-matrix
         run: echo "matrix=$(find tools -mindepth 1 -maxdepth 1 -type d | jq -R -s -c 'split("\n")[:-1] | map(split("/")[-1])')" >> "${GITHUB_OUTPUT}"
@@ -29,7 +29,7 @@ jobs:
          repo: ${{ fromJson(needs.list.outputs.matrix) }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
         with:
           token: ${{ secrets.USER_TOKEN }}
           ref: main