add nf-test tests and snapshots

.github/workflows/ci.yml

@@ -1,102 +1,89 @@
-name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+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: "0.8.3"
 
 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:
-  test:
-    name: Run pipeline with test data (AMP and ARG workflows)
-    # 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/funcscan') }}"
+  define_nxf_versions:
+    name: Choose nextflow versions to test against depending on target branch
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
-        parameters:
-          - "--annotation_tool prodigal"
-          - "--annotation_tool prokka"
-          - "--annotation_tool bakta --annotation_bakta_db_downloadtype light"
-
+    outputs:
+      matrix: ${{ steps.nxf_versions.outputs.matrix }}
     steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v3
-
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Run pipeline with test data (AMP and ARG workflows)
+      - id: nxf_versions
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
+          if [[ "${{ 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_bgc:
-    name: Run pipeline with test data (BGC workflow)
-    # 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/funcscan') }}"
+  test:
+    name: nf-test
+    needs: define_nxf_versions
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
-        parameters:
-          - "--annotation_tool prodigal"
-          - "--annotation_tool prokka"
-          - "--annotation_tool bakta --annotation_bakta_db_downloadtype light"
+        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
+        #components:
+        #  - "tests/pipeline/test.nf.test --profile test"
+        #parameters:
+        #  - "--annotation_tool prodigal"
+        #  - "--annotation_tool prokka"
+        #  - "--annotation_tool bakta --annotation_bakta_db_downloadtype light"
+        tags:
+          - "test"
+        #  - "test_bgc"
+        #  - "test_deeparg"
+        #  - "test_nothing"
+        #  - "test_full"
+        profile:
+          - "docker"
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Run pipeline with test data (BGC workflow)
+      - name: Install nf-test
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_bgc,docker --outdir ./results ${{ matrix.parameters }} --bgc_skip_deepbgc
+          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
+          sudo mv nf-test /usr/local/bin/
 
-  test_deeparg:
-    name: Run pipeline with test data (DeepARG only workflow)
-    # 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/funcscan') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
-        parameters:
-          - "--annotation_tool bakta --annotation_bakta_db_downloadtype light"
-          - "--annotation_tool pyrodigal"
+      - name: Run nf-test
+        run: |
+          nf-test test ${{ matrix.tags }},${{ matrix.profile }} --junitxml=test.xml
 
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml
 
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
         with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Run pipeline with test data (DeepARG workflow)
-        run: |
-          wget https://zenodo.org/record/8280582/files/deeparg.zip ## download from zenodo due to instability of deepARG server
-          unzip deeparg.zip
-          nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }} --arg_deeparg_data 'deeparg/'
+          report_paths: "*.xml"

.gitignore

@@ -6,4 +6,5 @@ results/
 testing/
 testing*
 *.pyc
-tests/
+nf-test/
+.nf-test*

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#323](https://github.com/nf-core/funcscan/pull/323) Add nf-test files and snapshots (by @louperelo)
 - [#322](https://github.com/nf-core/funcscan/pull/322) Updated all modules: introduce environment.yml files. (by @jasmezz)
 
 ### `Fixed`

conf/test_deeparg.config

@@ -32,6 +32,7 @@ params {
     arg_skip_amrfinderplus = true
     arg_skip_abricate      = true
     arg_skip_deeparg       = false
+    arg_deeparg_data       = 'https://zenodo.org/records/8280582/files/deeparg.zip?download=1'
 
     run_amp_screening      = false
     run_bgc_screening      = false

nf-test.config

@@ -0,0 +1,18 @@
+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/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/lib/UTILS.groovy

@@ -0,0 +1,38 @@
+// Helper functions for pipeline tests
+
+class UTILS {
+
+    // Function to remove Nextflow version from software_versions.yml
+    public static String removeNextflowVersion(outputDir) {
+        def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
+        if (softwareVersions.containsKey("Workflow")) {
+            softwareVersions.Workflow.remove("Nextflow")
+        }
+        return softwareVersions
+    }
+
+    // Function to filter lines from a file and return a new file
+    public static File filterLines(String inFilePath, int linesToSkip) {
+        if (linesToSkip >= 0) {
+            File inputFile = new File(inFilePath)
+            File outputFile = new File(inFilePath + ".filtered")
+            def lineCount = 0
+            inputFile.eachLine { line ->
+                lineCount++
+                if (lineCount > linesToSkip) {
+                    outputFile.append(line + '\n')
+                }
+            }
+            return outputFile
+        } else {
+            File inputFile = new File(inFilePath)
+            File outputFile = new File(inFilePath + ".filtered")
+            def lines = inputFile.readLines()
+            def totalLines = lines.size()
+            lines.take(totalLines + linesToSkip).each { line ->
+                outputFile.append(line + '\n')
+            }
+            return outputFile
+        }
+    }
+}

tests/pipeline/test.nf.test

@@ -0,0 +1,62 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "test"
+    tag "pipeline"
+
+    test("AMP and ARG workflow") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert snapshot(path("$outputDir/amp/ampir/").list()).match("amp_ampir") },
+                { assert snapshot(path("$outputDir/amp/amplify/").list()).match("amp_amplify") },
+                { assert new File("$outputDir/amp/hmmer_hmmsearch/sample_1/sample_1_mybacteriocin.txt.gz").exists() },
+                { assert new File("$outputDir/amp/hmmer_hmmsearch/sample_2/sample_2_mybacteriocin.txt.gz").exists() },
+                { assert snapshot(path("$outputDir/amp/macrel/sample_1/sample_1_log.txt"),
+                                path("$outputDir/amp/macrel/sample_1/README.md")).match("amp_macrel_sample_1") },
+                { assert new File("$outputDir/amp/macrel/sample_1/sample_1.all_orfs.faa.gz").exists() },
+                { assert new File("$outputDir/amp/macrel/sample_1/sample_1.prediction.gz").exists() },
+                { assert snapshot(path("$outputDir/amp/macrel/sample_2/sample_2_log.txt"),
+                                path("$outputDir/amp/macrel/sample_2/README.md")).match("amp_macrel_sample_2") },
+                { assert new File("$outputDir/amp/macrel/sample_2/sample_2.all_orfs.faa.gz").exists() },
+                { assert new File("$outputDir/amp/macrel/sample_2/sample_2.prediction.gz").exists() },
+                { assert snapshot(path("$outputDir/arg/abricate/").list()).match("arg_abricate") },
+                { assert snapshot(path("$outputDir/arg/amrfinderplus/").list()).match("arg_amrfinderplus") },
+                { assert snapshot(path("$outputDir/arg/fargene/sample_1/class_a/predictedGenes/wastewater_metagenome_contigs_1-class_A-filtered-peptides.fasta"),
+                                path("$outputDir/arg/fargene/sample_1/class_a/predictedGenes/wastewater_metagenome_contigs_1-class_A-filtered.fasta"),
+                                path("$outputDir/arg/fargene/sample_1/class_a/results_summary.txt"),
+                                path("$outputDir/arg/fargene/sample_1/class_b_1_2/predictedGenes/wastewater_metagenome_contigs_1-class_B_1_2-filtered-peptides.fasta"),
+                                path("$outputDir/arg/fargene/sample_1/class_b_1_2/predictedGenes/wastewater_metagenome_contigs_1-class_B_1_2-filtered.fasta"),
+                                path("$outputDir/arg/fargene/sample_1/class_b_1_2/results_summary.txt"),
+                                path("$outputDir/arg/fargene/sample_2/class_a/predictedGenes/wastewater_metagenome_contigs_2-class_A-filtered-peptides.fasta"),
+                                path("$outputDir/arg/fargene/sample_2/class_a/predictedGenes/wastewater_metagenome_contigs_2-class_A-filtered.fasta"),
+                                path("$outputDir/arg/fargene/sample_2/class_a/results_summary.txt"),
+                                path("$outputDir/arg/fargene/sample_2/class_b_1_2/predictedGenes/wastewater_metagenome_contigs_2-class_B_1_2-filtered-peptides.fasta"),
+                                path("$outputDir/arg/fargene/sample_2/class_b_1_2/predictedGenes/wastewater_metagenome_contigs_2-class_B_1_2-filtered.fasta"),
+                                path("$outputDir/arg/fargene/sample_2/class_b_1_2/results_summary.txt")).match("arg_fargene") },
+                { assert snapshot(path("$outputDir/arg/hamronization/").list()).match("arg_hamronization") },
+                { assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"),
+                                path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt")).match("multiqc") },
+                { assert new File("$outputDir/reports/ampcombi/ampcombi.log").exists() },
+                { assert new File("$outputDir/reports/ampcombi/sample_1/sample_1_amp.faa").exists() },
+                { assert new File("$outputDir/reports/ampcombi/sample_1/sample_1_ampcombi.csv").exists() },
+                { assert new File("$outputDir/reports/ampcombi/sample_1/sample_1_diamond_matches.txt").exists() },
+                { assert new File("$outputDir/reports/ampcombi/sample_2/sample_2_amp.faa").exists() },
+                { assert new File("$outputDir/reports/ampcombi/sample_2/sample_2_ampcombi.csv").exists() },
+                { assert new File("$outputDir/reports/ampcombi/sample_2/sample_2_diamond_matches.txt").exists() },
+                { assert snapshot(path("$outputDir/reports/hamronization_summarize/hamronization_combined_report.tsv")).match("summary_hamronization") }
+            )
+        }
+
+    }
+
+}