diff --git a/.github/workflows/ci-main.yml b/.github/workflows/ci-main.yml
index 926bd088f2d13d..5d6abd69f6bd64 100644
--- a/.github/workflows/ci-main.yml
+++ b/.github/workflows/ci-main.yml
@@ -25,7 +25,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 1000
           persist-credentials: false
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c05a8c3434b726..6893613095cf9a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name != 'pull_request' || !github.event.pull_request.draft
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 1
           persist-credentials: false
diff --git a/.github/workflows/cron-commit-cache.yml b/.github/workflows/cron-commit-cache.yml
index 47354c27dd0d80..4420a164a335f4 100644
--- a/.github/workflows/cron-commit-cache.yml
+++ b/.github/workflows/cron-commit-cache.yml
@@ -15,7 +15,7 @@ jobs:
       (github.event_name != 'pull_request' ||
        github.event.pull_request.head.repo.full_name == github.repository)
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 1000
           persist-credentials: false
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 15b560162b5f62..4e12e71ee1b21d 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.repository_owner == 'galaxyproject'
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           # Avg commits between successive monday:
           #  Min.   :  2.0
diff --git a/.github/workflows/git-gat.yml b/.github/workflows/git-gat.yml
index 78e44b532cdc41..960fc3b31eb73c 100644
--- a/.github/workflows/git-gat.yml
+++ b/.github/workflows/git-gat.yml
@@ -17,7 +17,7 @@ jobs:
   run:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 1
           persist-credentials: false
diff --git a/.github/workflows/google-form-events.yml b/.github/workflows/google-form-events.yml
index 469a4b56e5dfac..8a40d2df59fd8c 100644
--- a/.github/workflows/google-form-events.yml
+++ b/.github/workflows/google-form-events.yml
@@ -15,7 +15,7 @@ jobs:
       (github.event_name != 'pull_request' ||
        github.event.pull_request.head.repo.full_name == github.repository)
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 1
           persist-credentials: false
diff --git a/.github/workflows/google-form-faqs.yml b/.github/workflows/google-form-faqs.yml
index 18f106d6d9af89..e66ed02dc9254c 100644
--- a/.github/workflows/google-form-faqs.yml
+++ b/.github/workflows/google-form-faqs.yml
@@ -15,7 +15,7 @@ jobs:
       (github.event_name != 'pull_request' ||
        github.event.pull_request.head.repo.full_name == github.repository)
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 1
           persist-credentials: false
diff --git a/.github/workflows/google-form-news.yml b/.github/workflows/google-form-news.yml
index 823d3ffb4f0b60..1681d56b4ec08b 100644
--- a/.github/workflows/google-form-news.yml
+++ b/.github/workflows/google-form-news.yml
@@ -15,7 +15,7 @@ jobs:
       (github.event_name != 'pull_request' ||
        github.event.pull_request.head.repo.full_name == github.repository)
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 1
           persist-credentials: false
diff --git a/.github/workflows/google-form-recordings.yml b/.github/workflows/google-form-recordings.yml
index 48ca6e91b31d24..931cf6dc2f3617 100644
--- a/.github/workflows/google-form-recordings.yml
+++ b/.github/workflows/google-form-recordings.yml
@@ -15,7 +15,7 @@ jobs:
       (github.event_name != 'pull_request' ||
        github.event.pull_request.head.repo.full_name == github.repository)
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 1
           persist-credentials: false
diff --git a/.github/workflows/matrix.yml b/.github/workflows/matrix.yml
index 847f0a2d66892c..a9c4d32c80fc98 100644
--- a/.github/workflows/matrix.yml
+++ b/.github/workflows/matrix.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 200
           persist-credentials: false
diff --git a/.github/workflows/monthly-release-backfill.yml b/.github/workflows/monthly-release-backfill.yml
index 37f34008534203..d97f9c719fff40 100644
--- a/.github/workflows/monthly-release-backfill.yml
+++ b/.github/workflows/monthly-release-backfill.yml
@@ -24,7 +24,7 @@ jobs:
           docker-images: false
           swap-storage: false
 
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           ref: "${{ github.event.inputs.selected_tag }}"
           fetch-depth: 0
diff --git a/.github/workflows/monthly-release.yml b/.github/workflows/monthly-release.yml
index b95d24a46d2993..67be7e57835bfb 100644
--- a/.github/workflows/monthly-release.yml
+++ b/.github/workflows/monthly-release.yml
@@ -23,7 +23,7 @@ jobs:
           echo "release_title=$(LC_ALL=C date '+%Y %B %d')" >> $GITHUB_ENV
           echo "release_tag=$(LC_ALL=C date -I)" >> $GITHUB_ENV
 
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           # Based on logic in deploy.yml
           fetch-depth: 1200
diff --git a/.github/workflows/optimize-images.yml b/.github/workflows/optimize-images.yml
index 9242bfb107dfe2..9b3f8b58f11c3b 100644
--- a/.github/workflows/optimize-images.yml
+++ b/.github/workflows/optimize-images.yml
@@ -24,7 +24,7 @@ jobs:
        github.event.pull_request.head.repo.full_name == github.repository)
     steps:
       - name: Checkout Branch
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
         with:
           persist-credentials: false
 
diff --git a/.github/workflows/reviewdog-comment.yml b/.github/workflows/reviewdog-comment.yml
index 34a56f8827a86d..b16807a272738b 100644
--- a/.github/workflows/reviewdog-comment.yml
+++ b/.github/workflows/reviewdog-comment.yml
@@ -9,7 +9,7 @@ jobs:
   comment:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 1
           persist-credentials: false
diff --git a/.github/workflows/shortlinks.yaml b/.github/workflows/shortlinks.yaml
index c2a599e7a0b1df..8e55911319c9f8 100644
--- a/.github/workflows/shortlinks.yaml
+++ b/.github/workflows/shortlinks.yaml
@@ -15,7 +15,7 @@ jobs:
       (github.event_name != 'pull_request' ||
        github.event.pull_request.head.repo.full_name == github.repository)
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 10
           persist-credentials: false
diff --git a/.github/workflows/social.yml b/.github/workflows/social.yml
index 9ed91f490649f0..d156bbe687f776 100644
--- a/.github/workflows/social.yml
+++ b/.github/workflows/social.yml
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       # Shallow should be fine for video
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 500
           persist-credentials: false
diff --git a/.github/workflows/update-libraries.yaml b/.github/workflows/update-libraries.yaml
index 3754030a214f06..bba6cc5adda132 100644
--- a/.github/workflows/update-libraries.yaml
+++ b/.github/workflows/update-libraries.yaml
@@ -15,7 +15,7 @@ jobs:
       (github.event_name != 'pull_request' ||
        github.event.pull_request.head.repo.full_name == github.repository)
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 1
           persist-credentials: false
diff --git a/.github/workflows/video-dry.yml b/.github/workflows/video-dry.yml
index 8b1996dc27012a..968169d5d9647a 100644
--- a/.github/workflows/video-dry.yml
+++ b/.github/workflows/video-dry.yml
@@ -18,7 +18,7 @@ jobs:
       #     - 5002:5002
     steps:
       # Shallow should be fine for video
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 1
           persist-credentials: false
diff --git a/.github/workflows/video.yml b/.github/workflows/video.yml
index c49d8cabcf0546..f396e8caca1b8a 100644
--- a/.github/workflows/video.yml
+++ b/.github/workflows/video.yml
@@ -19,7 +19,7 @@ jobs:
           - 5002:5002
     steps:
       # Shallow should be fine for video
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 5000
           persist-credentials: false
diff --git a/.github/workflows/workflowhub.yml b/.github/workflows/workflowhub.yml
index d7f70a221550c3..3e8e7435900413 100644
--- a/.github/workflows/workflowhub.yml
+++ b/.github/workflows/workflowhub.yml
@@ -18,7 +18,7 @@ jobs:
       pull-requests: write
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 2000
           persist-credentials: false