Set up for nf-test

.github/workflows/ci.yml

@@ -40,3 +40,92 @@ jobs:
       - name: Run pipeline with test data
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+
+  changes:
+    name: Check for changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'tags' output variable
+      tags: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Combine all tags.yml files
+        id: get_username
+        run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml
+      - name: debug
+        run: cat .github/tags.yml
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: ".github/tags.yml"
+  nf-test:
+    name: nf-test ${{ matrix.tags }} ${{ matrix.profile }}
+    needs: [changes]
+    if: needs.changes.outputs.tags != '[]'
+    runs-on: ubuntu-latest
+    env:
+      TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }}
+    strategy:
+      fail-fast: false
+      matrix:
+        NXF_VER: ["23.10.0"]
+        tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
+        profile:
+          - "docker"
+          - "conda"
+
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v3
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Set up miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda setup
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Run nf-test
+        run: |
+          nf-test test --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml
+
+      - 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

modules/local/seqera_runs_dump/tests/main.nf.test

@@ -0,0 +1,38 @@
+nextflow_process {
+
+    name "Test Process SEQERA_RUNS_DUMP"
+    script "../main.nf"
+    process "SEQERA_RUNS_DUMP"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_local"
+    tag "seqera_runs_dump"
+
+    test("Should run without failures") {
+
+        when {
+            process {
+                """
+                input[0] = ['id': '4Bi5xBK6E2Nbhj', 'workspace': 'community/showcase']
+                input[1] = "https://api.tower.nf"
+                """
+            }
+        }
+
+        then {
+            def dumpFiles = file(process.out.run_dump.get(0).get(1)).listFiles().sort()
+
+            assertAll(
+                { assert snapshot(
+                    dumpFiles.grep { file -> ! file.name.matches("workflow-launch.json") },
+                    process.out.workflow_json
+                ).match()},
+                { assert dumpFiles.find { it.name.matches('workflow-launch.json')}.exists()},
+                { assert process.success }
+            )
+        }
+
+    }
+
+}

modules/local/seqera_runs_dump/tests/main.nf.test.snap

@@ -0,0 +1,15 @@
+{
+    "Should run without failures": {
+        "content": [
+            [
+                "service-info.json:md5,0a2624c21efb65b85e37fa3d07903dcc",
+                "workflow-load.json:md5,4f02d5a24ab89aa648cd4346785c8f2c",
+                "workflow-metrics.json:md5,70dd1af37145c8c2d23836fe850622e7",
+                "workflow-tasks.json:md5,577a7472816b7729012a9291d97ff150",
+                "workflow.json:md5,34db0e39f0246670eac77c7a5e9093c9"
+            ],
+            null
+        ],
+        "timestamp": "2023-11-29T13:34:09.5038157"
+    }
+}

modules/local/seqera_runs_dump/tests/nextflow.config

@@ -0,0 +1 @@
+process { withName: 'SEQERA_RUNS_DUMP' { container = 'quay.io/seqeralabs/nf-aggregate:tower-cli-0.9.0--2cb0f2e9d85d026b' } }

modules/local/seqera_runs_dump/tests/tags.yml

@@ -0,0 +1,2 @@
+seqera_runs_dump:
+  - modules/local/seqera_runs_dump/**

nf-test.config

@@ -0,0 +1,16 @@
+config {
+    // location for all nf-tests
+    testsDir "."
+
+    // nf-test directory including temporary files for each test
+    workDir "/tmp"
+
+    // location of library folder that is added automatically to the classpath
+    libDir "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 ""
+}

tests/nextflow.config

@@ -0,0 +1,5 @@
+/*
+========================================================================================
+    Nextflow config file for running tests
+========================================================================================
+*/