Merge pull request #231 from christopher-mohr/fix_ci_tests

Clean up CI tests
nf-core · Feb 16, 2024 · 14cafe5 · 14cafe5
2 parents b6d9cf4 + 1033fc8
commit 14cafe5
Showing 1 changed file with 17 additions and 37 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -42,32 +42,22 @@ jobs:
     name: Run profile tests
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/epitopeprediction') }}
     runs-on: ubuntu-latest
-    env:
-      NXF_VER: ${{ matrix.nxf_ver }}
-      NXF_ANSI_LOG: false
     strategy:
       matrix:
-        include:
-          # Test pipeline minimum Nextflow version
-          - NXF_VER: "22.10.1"
-            NXF_EDGE: ""
-          # Test latest edge release of Nextflow
-          - NXF_VER: ""
-            NXF_EDGE: "1"
+        NXF_VER:
+          - "23.04.0"
+          - "latest-everything"
         tests:
           ["test_grch38", "test_peptides", "test_peptides_h2", "test_proteins", "test_mhcnuggets", "test_mhcflurry"]
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
+
       - name: Install Nextflow
-        env:
-          NXF_VER: ${{ matrix.NXF_VER }}
-          # Uncomment only if the edge release is more recent than the latest stable release
-          # See https://github.com/nextflow-io/nextflow/issues/2467
-          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
       - name: Run pipeline with profile ${{ matrix.tests }}
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --outdir ./results
@@ -76,20 +66,14 @@ jobs:
     name: Run NetMHC tool family tests
     if: ${{ ( github.event_name == 'push' && github.repository == 'nf-core/epitopeprediction' ) || github.event.pull_request.head.repo.full_name == 'nf-core/epitopeprediction' }}
     runs-on: ubuntu-latest
-    env:
-      NXF_VER: ${{ matrix.nxf_ver }}
     strategy:
       matrix:
-        include:
-          # Test pipeline minimum Nextflow version
-          - NXF_VER: "22.10.1"
-            NXF_EDGE: ""
-          # Test latest edge release of Nextflow
-          - NXF_VER: ""
-            NXF_EDGE: "1"
+        NXF_VER:
+          - "23.04.0"
+          - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install non-free software
         env:
@@ -99,14 +83,10 @@ jobs:
           curl -L https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/software/non-free-software.tar.gpg | ${GITHUB_WORKSPACE}/bin/decrypt | tar -C non-free -v -x
 
       - name: Install Nextflow
-        env:
-          NXF_VER: ${{ matrix.NXF_VER }}
-          # Uncomment only if the edge release is more recent than the latest stable release
-          # See https://github.com/nextflow-io/nextflow/issues/2467
-          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
       - name: Run pipeline with NetMHC
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_netmhc,docker --outdir ./results