Merge branch 'dev' into add-force_pr-to-sync

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

@@ -17,7 +17,7 @@ runs:
 
     # Set up Nextflow
     - name: Install Nextflow
-      uses: nf-core/setup-nextflow@v1
+      uses: nf-core/setup-nextflow@v2
       with:
         version: ${{ matrix.NXF_VER }}
 

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

@@ -72,7 +72,7 @@ jobs:
           pip install .
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: latest-everything
 

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

@@ -59,7 +59,7 @@ jobs:
           pip install .
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: ${{ matrix.NXF_VER }}
 

.github/workflows/pytest.yml

@@ -119,7 +119,7 @@ jobs:
         run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
       - name: Look if nf-test is already installed and write to env variable
         id: check-nftest
@@ -133,7 +133,7 @@ jobs:
       - name: Cache nf-test installation
         if: env.nftest_installed != 'true'
         id: cache-software
-        uses: actions/cache@13aacd865c20de90d75de3b17ebe84f7a17d57d2 # v4
+        uses: actions/cache@ab5e6d0c87105b4c9c2047343972218f562e4319 # v4
         with:
           path: |
             /usr/local/bin/nf-test
@@ -197,7 +197,7 @@ jobs:
           mv .github/.coveragerc .
 
       - name: Download all artifacts
-        uses: actions/download-artifact@87c55149d96e628cc2ef7e6fc2aab372015aec85 # v4
+        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4
       - name: Run coverage
         run: |
           coverage combine --keep coverage*/.coverage*

.github/workflows/rich-codex.yml

@@ -15,11 +15,11 @@ jobs:
           cache-dependency-path: setup.py
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
       - name: Cache nf-test installation
         id: cache-software
-        uses: actions/cache@13aacd865c20de90d75de3b17ebe84f7a17d57d2 # v4
+        uses: actions/cache@ab5e6d0c87105b4c9c2047343972218f562e4319 # v4
         with:
           path: |
             /usr/local/bin/nf-test

.github/workflows/sync.yml

@@ -71,7 +71,7 @@ jobs:
           pip install .
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "latest-everything"
 

CHANGELOG.md

@@ -10,8 +10,10 @@
 
 ### General
 
+- Update CI to use nf-core/setup-nextflow v2
 - Changelog bot: handle also patch version before dev suffix ([#2820](https://github.com/nf-core/tools/pull/2820))
 - Add `force_pr` flag to sync, to force a PR even though there are no changes committed ([#2822](https://github.com/nf-core/tools/pull/2822))
+- Update GitHub Actions ([#2827](https://github.com/nf-core/tools/pull/2827))
 
 ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]