diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 67d1a54d4..5e2476c72 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -1,6 +1,11 @@
 name: Configs tests
-
-on: [pull_request, push]
+on:
+  pull_request:
+    branches:
+      - "*"
+  push:
+    branches:
+      - master
 
 # Cancel if a newer run is started
 concurrency:
@@ -17,15 +22,22 @@ jobs:
         run: python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml
 
   check_nextflow_config:
-    runs-on: ubuntu-latest
     name: Check if nextflow config runs in repository root
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        NXF_VER:
+          - 25.04.0
+          - latest-everything
     steps:
-      - uses: actions/checkout@v4
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-      - run: nextflow config -show-profiles ${GITHUB_WORKSPACE}
+        - uses: actions/checkout@v4
+        - name: Set up Nextflow
+          uses: nf-core/setup-nextflow@v2
+          with:
+            version: ${{ matrix.NXF_VER }}
+        - run: nextflow config -show-profiles ${GITHUB_WORKSPACE}
+        - run: nextflow lint ${GITHUB_WORKSPACE}
 
   profile_test:
     runs-on: ubuntu-latest