Update GitHub Actions (major)

.github/actions/create-lint-wf/action.yml

@@ -82,7 +82,7 @@ runs:
 
     - name: Upload log file artifact
       if: ${{ always() }}
-      uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
       with:
         name: nf-core-log-file-${{ matrix.NXF_VER }}
         path: create-lint-wf/log.txt

.github/workflows/create-test-lint-wf-template.yml

@@ -196,7 +196,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: nf-core-log-file-${{ matrix.TEMPLATE }}
           path: create-test-lint-wf/artifact_files.tar

.github/workflows/create-test-wf.yml

@@ -90,7 +90,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: nf-core-log-file-${{ matrix.NXF_VER }}
           path: create-test-wf/log.txt

.github/workflows/pytest.yml

@@ -133,15 +133,15 @@ jobs:
           echo "test=${test}" >> $GITHUB_ENV
 
       - name: Store snapshot report
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         if: always() && contains(matrix.test, 'test_create_app') && steps.pytest.outcome == 'failure'
         with:
           include-hidden-files: true
           name: Snapshot Report ${{ env.test }}
           path: ./snapshot_report.html
 
       - name: Upload coverage
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           include-hidden-files: true
           name: coverage_${{ env.test }}
@@ -169,7 +169,7 @@ jobs:
           mv .github/.coveragerc .
 
       - name: Download all artifacts
-        uses: actions/download-artifact@634f93cb2916e3fdff6788551b99b062d0335ce0 # v5
+        uses: actions/download-artifact@018cc2cf5baa6db3ef3c5f8a56943fffe632ef53 # v6
         with:
           pattern: coverage_*
 

.github/workflows/sync.yml

@@ -117,7 +117,7 @@ jobs:
 
       - name: Upload sync log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: sync_log_${{ matrix.pipeline }}
           path: sync_log_${{ matrix.pipeline }}.txt

CHANGELOG.md

@@ -4,6 +4,8 @@
 
 ### General
 
+- Update GitHub Actions (major) ([#3849](https://github.com/nf-core/tools/pull/3849))
+
 ### Template
 
 ### Linting

nf_core/pipeline-template/.github/workflows/awsfulltest.yml

@@ -40,7 +40,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |

nf_core/pipeline-template/.github/workflows/awstest.yml

@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |

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@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: nextflow_logfile.txt
           path: .nextflow.log*

nf_core/pipeline-template/.github/workflows/linting.yml

@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: linting-logs
           path: |