diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
index dd5ff6e347..3ade34c813 100644
--- a/.github/workflows/changelog.yml
+++ b/.github/workflows/changelog.yml
@@ -85,7 +85,7 @@ jobs:
 
       - name: Run pre-commit rules with prek
         if: steps.file_changed.outputs.changed == 'TRUE'
-        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
+        uses: j178/prek-action@4e14d07f9231acabce116ccfca13b13dd9755ece # v3.0.0
         continue-on-error: true
         with:
           extra-args: --config ${{ runner.temp }}/pre-commit-config.yaml --files CHANGELOG.md
diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml
index 0667bcd659..fe50f66eb4 100644
--- a/.github/workflows/codspeed.yml
+++ b/.github/workflows/codspeed.yml
@@ -42,7 +42,7 @@ jobs:
           version: ${{ github.event.inputs.nextflow-version || matrix.nextflow-version }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           enable-cache: true
 
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index c078ac4068..a2a9f0dca4 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -52,7 +52,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           enable-cache: true
 
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 9c101fbdd5..0b87823b07 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -64,7 +64,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           enable-cache: true
 
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 9a3774ac2b..7fee342be8 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -50,7 +50,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           enable-cache: true
 
diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
index 8786b5a084..15fbb56bf7 100644
--- a/.github/workflows/deploy-pypi.yml
+++ b/.github/workflows/deploy-pypi.yml
@@ -22,7 +22,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           enable-cache: true
 
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 4415e97907..738e69acd1 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -33,7 +33,7 @@ jobs:
       # Install and run prek
       - name: Run prek
         id: prek
-        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
+        uses: j178/prek-action@4e14d07f9231acabce116ccfca13b13dd9755ece # v3.0.0
         with:
           extra-args: --config .pre-commit-config.yaml --all-files
         continue-on-error: true
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index 681c5563a5..f223f32b3f 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -22,6 +22,6 @@ jobs:
       - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Run prek
-        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
+        uses: j178/prek-action@4e14d07f9231acabce116ccfca13b13dd9755ece # v3.0.0
         with:
           extra-args: --config .pre-commit-config.yaml --all-files
diff --git a/.github/workflows/nextflow-source-test.yml b/.github/workflows/nextflow-source-test.yml
index 649fdc42dc..3dfa2c1a23 100644
--- a/.github/workflows/nextflow-source-test.yml
+++ b/.github/workflows/nextflow-source-test.yml
@@ -50,7 +50,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           enable-cache: true
 
diff --git a/.github/workflows/pr-comment.yml b/.github/workflows/pr-comment.yml
index 8d16a65daf..342aee5f60 100644
--- a/.github/workflows/pr-comment.yml
+++ b/.github/workflows/pr-comment.yml
@@ -29,7 +29,7 @@ jobs:
     if: github.event.workflow_run.event == 'pull_request'
     steps:
       - name: Download PR comment artifact
-        uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21
+        uses: dawidd6/action-download-artifact@57aa996fc1713cc1579039614f4645a7f4841fd4 # v23
         with:
           run_id: ${{ github.event.workflow_run.id }}
           name: pr-comment
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index fd2f04dd2d..68d80cf71a 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -82,7 +82,7 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           enable-cache: true
 
diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 7d9cf05901..e69a25eb6e 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -82,7 +82,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           enable-cache: true
 
diff --git a/.github/workflows/update-template-snapshots.yml b/.github/workflows/update-template-snapshots.yml
index 8adbcda40e..72f394d2f1 100644
--- a/.github/workflows/update-template-snapshots.yml
+++ b/.github/workflows/update-template-snapshots.yml
@@ -61,7 +61,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           enable-cache: true
 
diff --git a/.github/workflows/update-textual-snapshots.yml b/.github/workflows/update-textual-snapshots.yml
index fe029d48b9..c1e68d0421 100644
--- a/.github/workflows/update-textual-snapshots.yml
+++ b/.github/workflows/update-textual-snapshots.yml
@@ -42,7 +42,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           enable-cache: true
 
diff --git a/nf_core/pipeline-template/.github/workflows/fix_linting.yml b/nf_core/pipeline-template/.github/workflows/fix_linting.yml
index 4c91656253..3a0ee37570 100644
--- a/nf_core/pipeline-template/.github/workflows/fix_linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/fix_linting.yml
@@ -37,7 +37,7 @@ jobs:
       # Install and run prek
       - name: Run prek
         id: prek
-        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
+        uses: j178/prek-action@4e14d07f9231acabce116ccfca13b13dd9755ece # v3.0.0
         continue-on-error: true
 
       # indication that the linting has finished
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index 80c7055ef1..ec9344ea14 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -17,7 +17,7 @@ jobs:
         uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
       - name: Run prek
-        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
+        uses: j178/prek-action@4e14d07f9231acabce116ccfca13b13dd9755ece # v3.0.0
 
   nf-core:
     runs-on: ubuntu-latest
@@ -34,7 +34,7 @@ jobs:
           architecture: "x64"
 
       - name: Setup uv
-        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
 
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
diff --git a/nf_core/pipeline-template/.github/workflows/pr-comment.yml b/nf_core/pipeline-template/.github/workflows/pr-comment.yml
index c0a8c61e71..3773390a51 100644
--- a/nf_core/pipeline-template/.github/workflows/pr-comment.yml
+++ b/nf_core/pipeline-template/.github/workflows/pr-comment.yml
@@ -31,7 +31,7 @@ jobs:
     if: github.event.workflow_run.event == 'pull_request'
     steps:
       - name: Download PR comment artifact
-        uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21
+        uses: dawidd6/action-download-artifact@57aa996fc1713cc1579039614f4645a7f4841fd4 # v23
         with:{% raw %}
           run_id: ${{ github.event.workflow_run.id }}
           name: pr-comment