nf-test init

.github/workflows/ci.yml

@@ -1,40 +1,98 @@
 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:
+  pull_request:
     branches:
       - dev
-  pull_request:
   release:
     types: [published]
 
 env:
   NXF_ANSI_LOG: false
 
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
-  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/demultiplex') }}"
+  changes:
+    name: Check for changes
     runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      tags: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/tags.yml"
+
+  test_changes:
+    name: ${{ matrix.tags }} ${{ matrix.component }} ${{ matrix.profile }} ${{ matrix.NXF_VER }}
+    runs-on: ubuntu-20.04
+    needs: changes
+    if: needs.changes.outputs.tags != '[]'
     strategy:
+      fail-fast: false
       matrix:
         NXF_VER:
           - "21.10.3"
           - "latest-everything"
-        test:
-          - "test_bclconvert"
-          - "test_bcl2fastq"
-          - "test_bases2fastq"
+        tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
+        profile: ["docker"] # TODO Add singularity/conda
+        component: ["pipeline"] # TODO There aren't any subworkflows or modules tests YET
+        exclude:
+          - NXF_VER: "latest-everything"
+            profile: "conda"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+      - uses: actions/cache@v2
         with:
-          version: "${{ matrix.NXF_VER }}"
+          path: /usr/local/bin/
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
 
-      - name: Run pipeline with test data
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test }},docker --outdir ./results
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Install nf-test
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v5
+        with:
+          singularity-version: 3.7.1
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda clean
+        if: matrix.profile == 'conda'
+        run: conda clean -a
+
+      - name: Run nf-test
+        run: nf-test test --profile=test,${{ matrix.profile }} tests/${{ matrix.component }}/${{ matrix.tags }}/*.nf.test --junitxml=${{ matrix.tags }}.xml
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: "${{ matrix.tags }}.xml"

.gitignore

@@ -6,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+.nf-test/

.nf-core.yml

@@ -1 +1,3 @@
 repository_type: pipeline
+lint:
+  actions_ci: False

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#63](https://github.com/nf-core/demultiplex/pull/63) Replace fastqc with falco for speedier QC, fixes Replace fastqc with falco #62
 - [#64](https://github.com/nf-core/demultiplex/pull/64) Add subway map by @nvnieuwk
 - [#70](https://github.com/nf-core/demultiplex/pull/70) Make tools and trimming optional
+- [#71](https://github.com/nf-core/demultiplex/pull/71) Add nf-test
 
 ### `Fixed`
 
@@ -24,9 +25,9 @@ Initial release of nf-core/demultiplex, created with the [nf-core](https://nf-co
 
 ### `Added`
 
-- [#38](https://github.com/nf-core/demultiplex/pull/38) - Add FastP
-- [#39](https://github.com/nf-core/demultiplex/pull/39) - Add FastQC
-- [#51](https://github.com/nf-core/demultiplex/pull/51) - Add bases2fastq
+- [#38](https://github.com/nf-core/demultiplex/pull/38) Add FastP
+- [#39](https://github.com/nf-core/demultiplex/pull/39) Add FastQC
+- [#51](https://github.com/nf-core/demultiplex/pull/51) Add bases2fastq
 
 ### `Fixed`
 

README.md

@@ -7,6 +7,7 @@
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/demultiplex)
+[![nf-test](https://img.shields.io/badge/tested_with-nf--test-337ab7.svg)](https://github.com/askimed/nf-test)
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23demultiplex-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/demultiplex)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 

conf/test.config

@@ -32,33 +32,39 @@ process {
             "--force",
             "--first-tile-only true"
         ].join(" ").trim()}
-    }
-    publishDir = [
-        [
-            // Gather and write InterOp files
-            path: { "${params.outdir}/${meta.id}/InterOp" },
-            mode: params.publish_dir_mode,
-            pattern: "**.bin",
-            saveAs: {filename -> filename.split("/")[-1] }
-        ],
-        [
-            // Fetch RunInfo.xml
-            path: { "${params.outdir}/${meta.id}" },
-            mode: params.publish_dir_mode,
-            pattern: "RunInfo.xml",
-            overwrite: true,
-            saveAs: {filename -> filename.split("/")[-1] }
-        ],
-        [
-            // Gather and write Reports
-            path: { meta.lane ? "${params.outdir}/${meta.id}/L00${meta.lane}" : "${params.outdir}/${meta.id}" },
-            mode: params.publish_dir_mode,
-            pattern: "Reports",
-            saveAs: {filename -> filename.split("/")[-1] }
-        ],
-        [
-            path: { "${params.outdir}/${meta.id}" },
-            pattern: "**.fastq.gz",
+        publishDir = [
+            [
+                // Gather and write InterOp files
+                path: { "${params.outdir}/${meta.id}/InterOp" },
+                mode: params.publish_dir_mode,
+                pattern: "**.bin",
+                saveAs: {filename -> filename.split("/")[-1] }
+            ],
+            [
+                // Fetch RunInfo.xml
+                path: { "${params.outdir}/${meta.id}" },
+                mode: params.publish_dir_mode,
+                pattern: "RunInfo.xml",
+                overwrite: true,
+                saveAs: {filename -> filename.split("/")[-1] }
+            ],
+            [
+                // Gather and write Reports
+                path: { meta.lane ? "${params.outdir}/${meta.id}/L00${meta.lane}" : "${params.outdir}/${meta.id}" },
+                mode: params.publish_dir_mode,
+                pattern: "Reports",
+                saveAs: {filename -> filename.split("/")[-1] }
+            ],
+            [
+                path: { "${params.outdir}/${meta.id}" },
+                pattern: "**.fastq.gz",
+            ]
         ]
-    ]
+    }
+
+    withName: BCL2FASTQ {
+        ext.args = {[
+            "--tiles s_1_1101",
+        ].join(" ").trim()}
+    }
 }

nf-test.config

@@ -0,0 +1,8 @@
+config {
+
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "nextflow.config"
+    profile "test"
+
+}

tests/config/tags.yml

@@ -0,0 +1,10 @@
+default:
+  - bin/**
+  - conf/**
+  - lib/**
+  - modules/**
+  - subworkflows/**
+  - tests/**
+  - workflows/**
+  - nextflow.config
+  - main.nf

tests/pipeline/default/bases2fastq.nf.test

@@ -0,0 +1,38 @@
+nextflow_pipeline {
+
+    name "Test Bases2Fastq"
+    script "main.nf"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                input = "$baseDir/assets/inputs/b2fq-samplesheet.csv"
+                demultiplexer = 'bases2fastq'
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.succeeded().size() == 6
+
+            assert snapshot(
+                path("$outputDir/sim-data/DefaultSample_R1.fastq.gz.md5"),
+                path("$outputDir/sim-data/DefaultSample_R2.fastq.gz.md5"),
+                path("$outputDir/sim-data/Metrics.csv"),
+                path("$outputDir/sim-data/RunManifest.json"),
+                path("$outputDir/sim-data/UnassignedSequences.csv"),
+
+                path("$outputDir/sim-data/Samples/DefaultSample/DefaultSample_R1.fastq.gz"),
+                path("$outputDir/sim-data/Samples/DefaultSample/DefaultSample_R2.fastq.gz"),
+            ).match()
+
+            assert new File("$outputDir/sim-data/Bases2Fastq-Sim_QC.html").exists()
+            assert new File("$outputDir/sim-data/RunStats.json").exists()
+            assert new File("$outputDir/sim-data/Samples/DefaultSample/DefaultSample_stats.json").exists()
+        }
+
+    }
+
+}

tests/pipeline/default/bases2fastq.nf.test.snap

@@ -0,0 +1,14 @@
+{
+    "Should run without failures": {
+        "content": [
+            "DefaultSample_R1.fastq.gz.md5:md5,5d8bc31e54f78babafb9a860be2ff52a",
+            "DefaultSample_R2.fastq.gz.md5:md5,1b71d1475ec7fb7e7ca16b7958990622",
+            "Metrics.csv:md5,3213ad7bdf66f33476cb589b4d608948",
+            "RunManifest.json:md5,d4ecdb19e5fbcffab3e6e770c34023fb",
+            "UnassignedSequences.csv:md5,11c1693830ce941b8cfb8d2431a59097",
+            "DefaultSample_R1.fastq.gz:md5,77b68ec94323741d1bddc03a7a428fa9",
+            "DefaultSample_R2.fastq.gz:md5,ecd4ed53e10207582bbbc29383080b57"
+        ],
+        "timestamp": "2022-11-24T01:47:50+0000"
+    }
+}

tests/pipeline/default/bcl2fastq.nf.test

@@ -0,0 +1,30 @@
+nextflow_pipeline {
+
+    name "Test bcl2fastq"
+    script "main.nf"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                input = "${baseDir}/assets/inputs/flowcell_input.csv"
+                demultiplexer = 'bcl2fastq'
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.succeeded().size() == 5
+
+            assert snapshot(
+                path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz.md5"),
+
+                path("$outputDir/bcl2fastq/Sample1_S1_L001_R1_001.fastq.gz"),
+                path("$outputDir/bcl2fastq/Stats").list(),
+            ).match()
+        }
+
+    }
+
+}

tests/pipeline/default/bcl2fastq.nf.test.snap

@@ -0,0 +1,17 @@
+{
+    "Should run without failures": {
+        "content": [
+            "Sample1_S1_L001_R1_001.fastq.gz.md5:md5,2ffef70ffda3328c3c6607bf14ca50c3",
+            "Sample1_S1_L001_R1_001.fastq.gz:md5,e92fce7b86c6447b053d72c5cb4be89c",
+            [
+                "AdapterTrimming.txt:md5,48ed2b914b1246c0b5d8667525550946",
+                "ConversionStats.xml:md5,8fe0f57f3f5d256a0762dba75ac62d05",
+                "DemultiplexingStats.xml:md5,2047ff18f5b9107c084de06e9ff943ad",
+                "DemuxSummaryF1L1.txt:md5,03e5fd0c1e3079c5f8c7b4d0501b37ff",
+                "FastqSummaryF1L1.txt:md5,0c6f2d87ee183b84d1051cde9a5643d1",
+                "Stats.json:md5,8e5f038b8aa9e465599d3575f930e604"
+            ]
+        ],
+        "timestamp": "2022-11-24T01:58:20+0000"
+    }
+}

tests/pipeline/default/bclconvert.nf.test

@@ -0,0 +1,30 @@
+nextflow_pipeline {
+
+    name "Test bclconvert"
+    script "main.nf"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                input = "$baseDir/assets/inputs/flowcell_input.csv"
+                demultiplexer = 'bclconvert'
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert workflow.trace.succeeded().size() == 5
+
+            assert snapshot(
+                path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz"),
+                path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz.md5"),
+                path("$outputDir/220422_M11111_0222_000000000-K9H97/Undetermined_S0_L001_R1_001.fastq.gz"),
+                path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(),
+            ).match()
+        }
+
+    }
+
+}