Merge branch 'nf-test_implementation' into ci_test_branch_nf-core

.github/workflows/ci.yml

@@ -3,47 +3,30 @@ name: nf-core CI
 on:
   push:
     branches:
-      - "dev"
+      - dev
   pull_request:
-    branches:
-      - "dev"
-      - "master"
   release:
-    types:
-      - "published"
+    types: [published]
 
 env:
   NXF_ANSI_LOG: false
-  NFTEST_VER: "0.7.3"
+  NFTEST_VER: "0.8.4"
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
-  define_nxf_versions:
-    name: Choose nextflow versions to test against depending on target branch
-    runs-on: ubuntu-latest
-    outputs:
-      matrix: ${{ steps.nxf_versions.outputs.matrix }}
-    steps:
-      - id: nxf_versions
-        run: |
-          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
-            echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
-          else
-            echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT
-          fi
-
   test_profile_standard:
     name: nf-test with standard profiles
-    needs: define_nxf_versions
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
-        tags:
+        NXF_VER:
+          - "23.04.0"
+          - "latest-everything"
+        profile:
           - "test"
           - "test_model_information"
           - "test_mouse_all_pep_lengths"
@@ -53,30 +36,11 @@ jobs:
           - "test_mhcflurry"
           - "test_mhcnuggets_1"
           - "test_mhcnuggets_2"
-        profile:
-          - "docker"
 
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
-      - name: Check out test data
-        uses: actions/checkout@v3
-        with:
-          repository: nf-core/test-datasets
-          ref: metapep
-          path: test-datasets/
-          fetch-depth: 1
-
-      - name: Replace remote paths in samplesheets
-        run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheets/v1.0/*.csv; do
-            sed -i "s=https://github.com/nf-core/test-datasets/tree/metapep/testdata/=${{ github.workspace }}/test-datasets/=g" $f
-            echo "========== $f ============"
-            cat $f
-            echo "========================================"
-          done;
-
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
@@ -92,7 +56,7 @@ jobs:
 
       - name: Run nf-test
         run: |
-          nf-test test --tag ${{ matrix.tags }} --profile ${{ matrix.tags }},${{ matrix.profile }} --junitxml=test.xml
+          nf-test test --tag ${{ matrix.profile }} --profile ${{ matrix.profile }},docker --junitxml=test.xml
 
       - name: Output log on failure
         if: failure()
@@ -106,46 +70,28 @@ jobs:
         with:
           report_paths: "*.xml"
 
-  profile_download:
+  test_profile_download:
     name: nf-test with profiles needing entrez downloads
     # Only run on PRs from branches of nf-core/metapep repository or on push if this is the nf-core dev branch (merged PRs)
     # (GitHub secrets are not accessible for workflows from forks)
-    if: ${{ github.event.pull_request.head.repo.full_name == 'nf-core/metapep' || (github.event_name == 'push' && github.repository == 'nf-core/metapep') }}
-    needs: define_nxf_versions
+    if: "${{ github.event.pull_request.head.repo.full_name == 'nf-core/metapep' || (github.event_name == 'push' && github.repository == 'nf-core/metapep') }}"
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
-        tags:
+        NXF_VER:
+          - "23.04.0"
+          - "latest-everything"
+        profile:
           - "test_all"
           - "test_mouse"
           - "test_taxa_only"
           - "test_taxa_specific_assembly"
-        profile:
-          - "docker"
 
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
-      - name: Check out test data
-        uses: actions/checkout@v3
-        with:
-          repository: nf-core/test-datasets
-          ref: metapep
-          path: test-datasets/
-          fetch-depth: 1
-
-      - name: Replace remote paths in samplesheets
-        run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheets/v1.0/*.csv; do
-            sed -i "s=https://github.com/nf-core/test-datasets/tree/metapep/testdata/=${{ github.workspace }}/test-datasets/=g" $f
-            echo "========== $f ============"
-            cat $f
-            echo "========================================"
-          done;
-
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
@@ -164,7 +110,7 @@ jobs:
           NCBI_EMAIL: ${{ secrets.NCBI_EMAIL }}
           NCBI_KEY: ${{ secrets.NCBI_KEY }}
         run: |
-          nf-test test --tag ${{ matrix.tags }} --profile ${{ matrix.tags }},${{ matrix.profile }} --junitxml=test.xml
+          nf-test test --tag ${{ matrix.profile }} --profile ${{ matrix.profile }},docker --junitxml=test.xml
 
       - name: Output log on failure
         if: failure()

.nf-core.yml

@@ -2,4 +2,3 @@ repository_type: pipeline
 lint:
   files_exist:
     - conf/igenomes.config
-  actions_ci: False

modules.json

@@ -27,7 +27,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {