diff --git a/.github/actions/create-lint-wf/action.yml b/.github/actions/create-lint-wf/action.yml
index 4ef0a0cd5b..6556cc11b3 100644
--- a/.github/actions/create-lint-wf/action.yml
+++ b/.github/actions/create-lint-wf/action.yml
@@ -88,7 +88,7 @@ runs:
 
     - name: Upload log file artifact
       if: ${{ always() }}
-      uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+      uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6
       with:
         name: nf-core-log-file-${{ matrix.NXF_VER }}
         path: create-lint-wf/log.txt
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 392c3e335c..56080c547c 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -200,7 +200,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6
         with:
           name: nf-core-log-file-${{ matrix.TEMPLATE }}
           path: create-test-lint-wf/artifact_files.tar
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 250b76ae20..532b4bcb10 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -93,7 +93,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6
         with:
           name: nf-core-log-file-${{ matrix.NXF_VER }}
           path: create-test-wf/log.txt
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 2532e8b1cf..8e303cb0f0 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -120,7 +120,7 @@ jobs:
           echo "test=${test}" >> $GITHUB_ENV
 
       - name: Store snapshot report
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6
         if: always() && contains(matrix.test, 'test_create_app') && steps.pytest.outcome == 'failure'
         with:
           include-hidden-files: true
@@ -128,7 +128,7 @@ jobs:
           path: ./snapshot_report.html
 
       - name: Upload coverage
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6
         with:
           include-hidden-files: true
           name: coverage_py${{ matrix.python-version }}_${{ env.test }}
@@ -154,7 +154,7 @@ jobs:
           mv .github/.coveragerc .
 
       - name: Download all artifacts
-        uses: actions/download-artifact@018cc2cf5baa6db3ef3c5f8a56943fffe632ef53 # v6
+        uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7
         with:
           pattern: coverage_*
 
diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index d33fb8622b..c29b5e2085 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -125,7 +125,7 @@ jobs:
 
       - name: Upload sync log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6
         with:
           name: sync_log_${{ matrix.pipeline }}
           path: sync_log_${{ matrix.pipeline }}.txt
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 66a77dd299..2f89f8f745 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,7 @@
 - Update GitHub Actions ([#3957](https://github.com/nf-core/tools/pull/3957))
 - Update astral-sh/setup-uv digest to ed21f2f ([#3959](https://github.com/nf-core/tools/pull/3959))
 - Update codecov/codecov-action digest to 671740a ([#3962](https://github.com/nf-core/tools/pull/3962))
+- Update GitHub Actions (major) ([#3971](https://github.com/nf-core/tools/pull/3971))
 
 ### Template
 
diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index 7e2eb970ac..5f8fb427ee 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -40,7 +40,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+      - uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/nf_core/pipeline-template/.github/workflows/awstest.yml b/nf_core/pipeline-template/.github/workflows/awstest.yml
index 7e6b7ffb4f..4d81ded33b 100644
--- a/nf_core/pipeline-template/.github/workflows/awstest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awstest.yml
@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+      - uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
index 9f3100c112..edf5012dc3 100644
--- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
+++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
@@ -127,7 +127,7 @@ jobs:
           fi{% endraw %}
 
       - name: Upload Nextflow logfile for debugging purposes
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6
         with:
           name: nextflow_logfile.txt
           path: .nextflow.log*
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index 78083609c5..16143eebb6 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -64,7 +64,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6
         with:
           name: linting-logs
           path: |