Feat/nf tests

.gitattributes

@@ -1,4 +1,5 @@
 *.config linguist-language=nextflow
 *.nf.test linguist-language=nextflow
+tests/**/*nf.test.snap linguist-generated
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated

.github/workflows/ci.yml

@@ -1,38 +1,58 @@
-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
   pull_request:
+    branches:
+      - dev
+      - master
   release:
-    types: [published]
+    types:
+      - "published"
 
 env:
   NXF_ANSI_LOG: false
+  NFTEST_VER: "0.7.3"
 
 concurrency:
   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", "22.10.1"]' | tee -a $GITHUB_OUTPUT
+          fi
+
   test:
-    name: Run pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}"
+    name: nf-test
+    needs: define_nxf_versions
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        NXF_VER:
-          - "22.10.1"
-          - "latest-everything"
-        parameters:
-          - "--preprocessing_qc_tool falco"
-          - "--shortread_qc_tool fastp"
-          - "--shortread_qc_tool adapterremoval"
-          - "--shortread_complexityfilter_tool bbduk"
-          - "--shortread_complexityfilter_tool prinseqplusplus"
+        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
+        components:
+          - "tests/pipeline/test.nf.test --profile test"
+          - "tests/pipeline/test_with_complexityfilter_fastp.nf.test --profile test"
+          - "tests/pipeline/test_with_complexityfilter_prinseqpluslplus.nf.test --profile test"
+          - "tests/pipeline/test_with_preprocessingqc_falco.nf.test --profile test"
+          - "tests/pipeline/test_with_shortreadqc_adapterremoval.nf.test --profile test"
+          - "tests/pipeline/krakenuniq.nf.test --profile test_krakenuniq"
+          - "tests/pipeline/malt.nf.test --profile test_nothing"
+        profile:
+          - "docker"
 
     steps:
       - name: Check out pipeline code
@@ -43,46 +63,50 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Show current locale
-        run: locale
+      - name: Install nf-test
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Run nf-test default
+        run: |
+          nf-test test ${{ matrix.components }},${{ matrix.profile }} --junitxml=test.xml
 
-      - name: Set UTF-8 enabled locale
+      - name: Output log on failure
+        if: failure()
         run: |
-          sudo locale-gen en_US.UTF-8
-          sudo update-locale LANG=en_US.UTF-8
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml
 
-      - name: Run pipeline with test data
-        uses: Wandalen/[email protected]
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
         with:
-          command: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
-          attempt_limit: 3
+          report_paths: "*.xml"
 
-  motus:
-    name: Test mOTUs with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
+  test_motus:
+    name: nf-test motus
+    needs: define_nxf_versions
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        NXF_VER:
-          - "22.10.1"
-          - "latest-everything"
+        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
+        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: Show current locale
-        run: locale
-
-      - name: Set UTF-8 enabled locale
+      - name: Install nf-test
         run: |
-          sudo locale-gen en_US.UTF-8
-          sudo update-locale LANG=en_US.UTF-8
+          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
+          sudo mv nf-test /usr/local/bin/
 
       - name: Prepare the database
         run: |
@@ -91,74 +115,12 @@ jobs:
           echo 'tool,db_name,db_params,db_path' > 'database_motus.csv'
           echo 'motus,db_mOTU,,db_mOTU' >> 'database_motus.csv'
 
-      - name: Run pipeline with test data
-        uses: Wandalen/[email protected]
-        with:
-          command: nextflow run ${GITHUB_WORKSPACE} -profile test_motus,docker --outdir ./results --databases ./database_motus.csv
-          attempt_limit: 3
-
-  krakenuniq:
-    name: Test KrakenUniq with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "22.10.1"
-          - "latest-everything"
-
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Show current locale
-        run: locale
-
-      - name: Set UTF-8 enabled locale
-        run: |
-          sudo locale-gen en_US.UTF-8
-          sudo update-locale LANG=en_US.UTF-8
-
-      - name: Run pipeline with test data
-        uses: Wandalen/[email protected]
-        with:
-          command: nextflow run ${GITHUB_WORKSPACE} -profile test_krakenuniq,docker --outdir ./results
-          attempt_limit: 3
-
-  malt:
-    name: Test MALT with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "22.10.1"
-          - "latest-everything"
-
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Show current locale
-        run: locale
-
-      - name: Set UTF-8 enabled locale
+      - name: Run nf-test motus
         run: |
-          sudo locale-gen en_US.UTF-8
-          sudo update-locale LANG=en_US.UTF-8
+          nf-test test ${{ matrix.profile }} --profile test_motus,${{ matrix.profile }} --junitxml=test.xml
 
-      - name: Run pipeline with test data
-        uses: Wandalen/[email protected]
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
         with:
-          command: nextflow run ${GITHUB_WORKSPACE} -profile test_nothing,docker --run_malt --input 'https://github.com/nf-core/test-datasets/raw/taxprofiler/samplesheet_shortreadsonly.csv' --outdir ./results
-          attempt_limit: 3
+          report_paths: "*.xml"

.gitignore

@@ -6,3 +6,5 @@ results/
 testing/
 testing*
 *.pyc
+.nf-test/
+nf-test

.nf-core.yml

@@ -1 +1,5 @@
 repository_type: pipeline
+lint:
+  files_unchanged:
+    - .gitattributes
+  actions_ci: False

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#309](https://github.com/nf-core/taxprofiler/pull/309) Implemented nf-tests for existing CI tests (added by @sateeshperi)
 - [#276](https://github.com/nf-core/taxprofiler/pull/276) Implemented batching in the KrakenUniq samples processing. (added by @Midnighter)
 - [#272](https://github.com/nf-core/taxprofiler/pull/272) Add saving of final 'analysis-ready-reads' to dedicated directory. (❤️ to @alexhbnr for reporting, added by @jfy133)
 - [#303](https://github.com/nf-core/taxprofiler/pull/303) Add support for taxpasta profile standardisation in single sample pipeline runs (❤️ to @artur-matysik for reporting, added by @jfy133)

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 ""
+}

tests/pipeline/krakenuniq.nf.test

@@ -0,0 +1,50 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "test_krakenuniq"
+    tag "krakenuniq"
+    tag "pipeline"
+
+    test("Kraken Uniq") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert new File("$outputDir/bbduk/2612_ERR5766176_B.bbduk.log").exists() },
+                { assert new File("$outputDir/bbduk/2612_ERR5766176.bbduk.log").exists() },
+                { assert new File("$outputDir/bbduk/2612_ERR5766180.bbduk.log").exists() },
+                { assert new File("$outputDir/bbduk/2613_ERR5766181.bbduk.log").exists() },
+                { assert snapshot(path("$outputDir/bowtie2/align/").list()).match("bowtie2/align/") },
+                { assert snapshot(path("$outputDir/fastp/2612_ERR5766176_B.fastp.json"),
+                                path("$outputDir/fastp/2612_ERR5766176.fastp.json"),
+                                path("$outputDir/fastp/2612_ERR5766180.fastp.json"),
+                                path("$outputDir/fastp/2613_ERR5766181.fastp.json")).match("fastp") },
+                { assert snapshot(path("$outputDir/filtlong/").list()).match("filtlong") },
+                { assert snapshot(UTILS.filterLines("$outputDir/krakenuniq/db6/2612.krakenuniq.report.txt", 1),
+                                UTILS.filterLines("$outputDir/krakenuniq/db6/2613_ERR5766181.krakenuniq.report.txt", 1),
+                                UTILS.filterLines("$outputDir/krakenuniq/db6/ERR3201952.krakenuniq.report.txt", 1),
+                                UTILS.filterLines("$outputDir/krakenuniq/db6/ERX5474930_ERR5766174_1.krakenuniq.report.txt", 1)).match("krakenuniq") },
+                { assert snapshot(path("$outputDir/multiqc/multiqc_data/bbduk.txt"),
+                                path("$outputDir/multiqc/multiqc_data/filtlong.txt"),
+                                path("$outputDir/multiqc/multiqc_data/multiqc_bowtie2.txt"),
+                                path("$outputDir/multiqc/multiqc_data/multiqc_fastp.txt"),
+                                path("$outputDir/multiqc/multiqc_data/multiqc_fastqc_1.txt"),
+                                path("$outputDir/multiqc/multiqc_data/multiqc_samtools_stats.txt"),
+                                path("$outputDir/multiqc/multiqc_data/porechop.txt")).match("multiqc") },
+                { assert snapshot(UTILS.filterLines("$outputDir/porechop/ERR3201952_ERR3201952.log", -3)).match("porechop") },
+                { assert snapshot(path("$outputDir/samtools/stats/").list()).match("samtools/stats/") },
+                { assert new File("$outputDir/taxpasta/krakenuniq_db6.tsv").exists() }
+            )
+        }
+
+    }
+
+}