diff --git a/.github/workflows/AWSMegatests.yml b/.github/workflows/AWSMegatests.yml
index 1166a640..b9c949a8 100644
--- a/.github/workflows/AWSMegatests.yml
+++ b/.github/workflows/AWSMegatests.yml
@@ -33,14 +33,14 @@ jobs:
       # limit it to push jobs to allow PR jobs to run concurrently.
       - name: Turnstyle
         if: ${{ github.event_name == 'push' }}
-        uses: softprops/turnstyle@807f6009e7cee5c2c9faa41ccef03a8bb24b06ab # v2
+        uses: softprops/turnstyle@15f9da4059166900981058ba251e0b652511c68f # v3
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
 
       - name: Install Python
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6
         with:
           python-version: 3.13.x
 
diff --git a/.github/workflows/backups.yml b/.github/workflows/backups.yml
index 0fa324e8..7e2149dc 100644
--- a/.github/workflows/backups.yml
+++ b/.github/workflows/backups.yml
@@ -51,7 +51,7 @@ jobs:
           echo "TARBALL_FILENAME=$TARBALL_FILENAME" >> $GITHUB_OUTPUT
 
       - name: setup aws cli
-        uses: aws-actions/configure-aws-credentials@e3dd6a429d7300a6a4c196c26e071d42e0343502 # v4
+        uses: aws-actions/configure-aws-credentials@61815dcd50bd041e203e49132bacad1fd04d2708 # v5
         with:
           role-to-assume: ${{ secrets.AWS_BACKUP_ROLE }}
           aws-region: eu-west-1
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index adce8e0e..ff31c364 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -14,8 +14,8 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+      - uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6
         with:
           python-version: "3.13"
       - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
diff --git a/.github/workflows/sync-test-datasets.yml b/.github/workflows/sync-test-datasets.yml
index 59efdbc1..bb8be868 100644
--- a/.github/workflows/sync-test-datasets.yml
+++ b/.github/workflows/sync-test-datasets.yml
@@ -19,7 +19,7 @@ jobs:
     steps:
       - name: Get pipeline names and filter branches
         id: get-branches
-        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
+        uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8
         with:
           script: |
             // Fetch pipeline names from nf-core website
@@ -65,7 +65,7 @@ jobs:
 
     steps:
       - name: Configure AWS credentials
-        uses: aws-actions/configure-aws-credentials@e3dd6a429d7300a6a4c196c26e071d42e0343502 # v4
+        uses: aws-actions/configure-aws-credentials@61815dcd50bd041e203e49132bacad1fd04d2708 # v5
         with:
           aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
           aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
@@ -101,7 +101,7 @@ jobs:
 
     steps:
       - name: Configure AWS credentials
-        uses: aws-actions/configure-aws-credentials@e3dd6a429d7300a6a4c196c26e071d42e0343502 # v4
+        uses: aws-actions/configure-aws-credentials@61815dcd50bd041e203e49132bacad1fd04d2708 # v5
         with:
           aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
           aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}