Initialized tests

.github/workflows/ci.yml

@@ -1,37 +1,56 @@
 name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
-  push:
-    branches:
-      - dev
   pull_request:
-  release:
-    types: [published]
 
 env:
   NXF_ANSI_LOG: false
+  NFT_VER: "0.8.4"
+  NFT_WORKDIR: "~"
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
-
 jobs:
+  nf-test-changes:
+    name: Check for changes
+    runs-on: ubuntu-latest
+    outputs:
+      nf_test_files: ${{ steps.list.outputs.components }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: List nf-test files
+        id: list
+        uses: adamrtalbot/[email protected]
+        with:
+          head: ${{ github.sha }}
+          base: origin/${{ github.base_ref }}
+          include: .github/include.yaml
+
+      - name: print list of nf-test files
+        run: |
+          echo ${{ steps.list.outputs.components }}
+
   test:
-    name: Run pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/smrnaseq') }}"
+    name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
+    needs: [nf-test-changes]
+    if: needs.nf-test-changes.outputs.nf_test_files != '[]'
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         NXF_VER:
-          - "23.04.0"
           - "latest-everything"
+          - "23.04"
+        nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
         profile:
-          - "test"
-          - "test_no_genome"
-          - "test_umi"
-          - "test_index"
+          - "docker"
+
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
@@ -41,9 +60,53 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          architecture: "x64"
+
+      - name: Install pdiff to see diff between nf-test snapshots
+        run: |
+          python -m pip install --upgrade pip
+          pip install pdiff
+
+      - uses: nf-core/setup-nf-test@v1
+
+      - name: Run nf-test
+        run: |
+          nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+
+      - uses: pcolby/tap-summary@v1
+        with:
+          path: >-
+            test.tap
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: test.xml
+
+  confirm-pass:
+    runs-on: ubuntu-latest
+    needs: [test]
+    if: always()
+    steps:
+      - name: All tests ok
+        if: ${{ !contains(needs.*.result, 'failure') }}
+        run: exit 0
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
 
-      - name: Run pipeline with test data
+      - name: debug-print
+        if: always()
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results
+          echo "toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"

.gitignore

@@ -7,3 +7,4 @@ testing/
 testing*
 *.pyc
 execution_trace*
+.nf-test*

nf-test.config

@@ -0,0 +1,16 @@
+config {
+    // location for all nf-tests
+    testsDir "tests"
+
+    // nf-test directory including temporary files for each test
+    workDir ".nf-test"
+
+    // location of library folder that is added automatically to the classpath
+    libDir "tests/pipeline/lib/"
+
+    // location of an optional nextflow.config file specific for executing tests
+    configFile "nextflow.config"
+
+    // run all test with the defined docker profile from the main nextflow.config
+    profile "docker"
+}

tests/lib/UTILS.groovy

@@ -0,0 +1,11 @@
+// Function to remove Nextflow version from software_versions.yml
+
+class UTILS {
+    public static String removeNextflowVersion(outputDir) {
+        def softwareVersions = path("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").yaml
+        if (softwareVersions.containsKey("Workflow")) {
+            softwareVersions.Workflow.remove("Nextflow")
+        }
+        return softwareVersions
+    }
+}