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

@@ -1,31 +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/chipseq') }}"
+    name: nf-test
+    needs: define_nxf_versions
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        NXF_VER:
-          - "22.10.1"
-          - "latest-everything"
+        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
+        tags:
+          - "test_profile"
+          - "test_skip_trimming"
+          - "test_skip_consensus_peaks"
+          - "test_aligner_bowtie2"
+          - "test_aligner_chromap"
+          - "test_aligner_star"
+        profile:
+          - "docker"
+
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3
@@ -35,51 +62,23 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Run pipeline with test data
+      - name: Install nf-test
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
+          sudo mv nf-test /usr/local/bin/
 
-  parameters:
-    name: Test workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/chipseq') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - "--skip_trimming"
-          - "--skip_consensus_peaks"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
+      - name: Run nf-test
         run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+          nf-test test --tag ${{ matrix.tags }} --profile test,${{ matrix.profile }} --junitxml=test.xml
 
-      - name: Run pipeline with various parameters
+      - name: Output log on failure
+        if: failure()
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} --outdir ./results
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml
 
-  aligners:
-    name: Test available aligners
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/chipseq') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        aligner:
-          - "bowtie2"
-          - "chromap"
-          - "star"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with the different aligners available
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{ matrix.aligner }} --outdir ./results
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          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

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/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 +1,43 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "test_profile"
+    tag "pipeline"
+
+    test("Default Test Profile") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert snapshot(path("$outputDir/bwa/mergedLibrary/SPT5_INPUT_REP1.mLb.clN.sorted.bam"),
+                                path("$outputDir/bwa/mergedLibrary/SPT5_INPUT_REP2.mLb.clN.sorted.bam"),
+                                path("$outputDir/bwa/mergedLibrary/SPT5_T0_REP1.mLb.clN.sorted.bam"),
+                                path("$outputDir/bwa/mergedLibrary/SPT5_T0_REP2.mLb.clN.sorted.bam"),
+                                path("$outputDir/bwa/mergedLibrary/SPT5_T15_REP1.mLb.clN.sorted.bam"),
+                                path("$outputDir/bwa/mergedLibrary/SPT5_T15_REP2.mLb.clN.sorted.bam")).match("bwa/mergedLibrary/") },
+                { assert new File("$outputDir/bwa/mergedLibrary/bigwig/").exists() },
+                { assert new File("$outputDir/bwa/mergedLibrary/deepTools/").exists() },
+                { assert new File("$outputDir/bwa/mergedLibrary/macs2/").exists() },
+                { assert new File("$outputDir/bwa/mergedLibrary/phantompeakqualtools/").exists() },
+                { assert new File("$outputDir/bwa/mergedLibrary/picard_metrics/").exists() },
+                { assert new File("$outputDir/bwa/mergedLibrary/samtools_stats/").exists() },
+                { assert new File("$outputDir/fastqc/").exists() },
+                { assert snapshot(path("$outputDir/genome").list()).match("genome") },
+                { assert new File("$outputDir/igv/").exists() },
+                { assert new File("$outputDir/multiqc/").exists() },
+                { assert new File("$outputDir/pipeline_info/").exists() },
+                { assert new File("$outputDir/trimgalore/").exists() }
+            )
+        }
+
+    }
+
+}

tests/pipeline/test_aligner_bowtie2.nf.test

@@ -0,0 +1,44 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "test_aligner_bowtie2"
+    tag "pipeline"
+
+    test("Aligner - Bowtie2") {
+
+        when {
+            params {
+                outdir  = "$outputDir"
+                aligner = "bowtie2"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert new File("$outputDir/bowtie2/mergedLibrary/SPT5_INPUT_REP1.mLb.clN.sorted.bam").exists() },
+                { assert new File("$outputDir/bowtie2/mergedLibrary/SPT5_INPUT_REP2.mLb.clN.sorted.bam").exists() },
+                { assert new File("$outputDir/bowtie2/mergedLibrary/SPT5_T0_REP1.mLb.clN.sorted.bam").exists() },
+                { assert new File("$outputDir/bowtie2/mergedLibrary/SPT5_T0_REP2.mLb.clN.sorted.bam").exists() },
+                { assert new File("$outputDir/bowtie2/mergedLibrary/SPT5_T15_REP1.mLb.clN.sorted.bam").exists() },
+                { assert new File("$outputDir/bowtie2/mergedLibrary/SPT5_T15_REP2.mLb.clN.sorted.bam").exists() },
+                { assert new File("$outputDir/bowtie2/mergedLibrary/bigwig/").exists() },
+                { assert new File("$outputDir/bowtie2/mergedLibrary/deepTools/").exists() },
+                { assert new File("$outputDir/bowtie2/mergedLibrary/macs2/").exists() },
+                { assert new File("$outputDir/bowtie2/mergedLibrary/phantompeakqualtools/").exists() },
+                { assert new File("$outputDir/bowtie2/mergedLibrary/picard_metrics/").exists() },
+                { assert new File("$outputDir/bowtie2/mergedLibrary/samtools_stats/").exists() },
+                { assert new File("$outputDir/fastqc/").exists() },
+                { assert snapshot(path("$outputDir/genome").list()).match("genome") },
+                { assert new File("$outputDir/igv/").exists() },
+                { assert new File("$outputDir/multiqc/").exists() },
+                { assert new File("$outputDir/pipeline_info/").exists() },
+                { assert new File("$outputDir/trimgalore/").exists() }
+            )
+        }
+
+    }
+
+}

tests/pipeline/test_aligner_chromap.nf.test

@@ -0,0 +1,44 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "test_aligner_chromap"
+    tag "pipeline"
+
+    test("Aligner - Chromap") {
+
+        when {
+            params {
+                outdir  = "$outputDir"
+                aligner = "chromap"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert snapshot(path("$outputDir/chromap/mergedLibrary/SPT5_INPUT_REP1.mLb.clN.sorted.bam"),
+                                path("$outputDir/chromap/mergedLibrary/SPT5_INPUT_REP2.mLb.clN.sorted.bam"),
+                                path("$outputDir/chromap/mergedLibrary/SPT5_T0_REP1.mLb.clN.sorted.bam"),
+                                path("$outputDir/chromap/mergedLibrary/SPT5_T0_REP2.mLb.clN.sorted.bam"),
+                                path("$outputDir/chromap/mergedLibrary/SPT5_T15_REP1.mLb.clN.sorted.bam"),
+                                path("$outputDir/chromap/mergedLibrary/SPT5_T15_REP2.mLb.clN.sorted.bam")).match("bwa/mergedLibrary/") },
+                { assert new File("$outputDir/chromap/mergedLibrary/bigwig/").exists() },
+                { assert new File("$outputDir/chromap/mergedLibrary/deepTools/").exists() },
+                { assert new File("$outputDir/chromap/mergedLibrary/macs2/").exists() },
+                { assert new File("$outputDir/chromap/mergedLibrary/phantompeakqualtools/").exists() },
+                { assert new File("$outputDir/chromap/mergedLibrary/picard_metrics/").exists() },
+                { assert new File("$outputDir/chromap/mergedLibrary/samtools_stats/").exists() },
+                { assert new File("$outputDir/fastqc/").exists() },
+                { assert snapshot(path("$outputDir/genome").list()).match("genome") },
+                { assert new File("$outputDir/igv/").exists() },
+                { assert new File("$outputDir/multiqc/").exists() },
+                { assert new File("$outputDir/pipeline_info/").exists() },
+                { assert new File("$outputDir/trimgalore/").exists() }
+            )
+        }
+
+    }
+
+}