Nf-test

.github/workflows/ci.yml

@@ -1,46 +1,48 @@
-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:
  release:
  types: [published]
+ merge_group:
+ types:
+ - checks_requested
+ branches:
+ - master
+ - dev
 
 env:
  NXF_ANSI_LOG: false
+ NFTEST_VER: "0.8.1"
 
 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
- # Only run on push if this is the nf-core dev branch (merged PRs)
+ name: "aligner: ${{ matrix.profile }} ; NF: ${{ matrix.NXF_VER }}"
  if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/scrnaseq') }}"
  runs-on: ubuntu-latest
  strategy:
+ fail-fast: false
  matrix:
  NXF_VER:
  - "23.04.0"
  - "latest-everything"
- profile: [
- "test,docker --aligner alevin",
- "test,docker --aligner kallisto",
- "test,docker --aligner star",
- "test,docker --aligner cellranger",
- # "test,docker --aligner cellrangerarc", // this currently lacks a suitable test profile, see issue https://github.com/nf-core/scrnaseq/issues/290
- # "test,docker --aligner universc", // this is broken, see issue https://github.com/nf-core/scrnaseq/issues/289
- ]
+ profile: ["alevin", "cellranger", "kallisto", "star"]
+
  steps:
  - name: Free some space
  run: |
  sudo rm -rf /usr/share/dotnet
  sudo rm -rf /opt/ghc
  sudo rm -rf "/usr/local/share/boost"
  sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+
  - name: Check out pipeline code
  uses: actions/checkout@v4
 
@@ -49,8 +51,33 @@ jobs:
  with:
  version: "${{ matrix.NXF_VER }}"
 
- - name: Run pipeline with test data
- # For example: adding multiple test runs with different parameters
- # Remember that you can parallelise this by using strategy.matrix
+ - 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: |
- nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }} --outdir ./results
+ nf-test test tests/main_pipeline_${{ matrix.profile }}.test --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

.gitignore

@@ -9,3 +9,4 @@ testing*
 log/
 reports/
 testme.sh
+.nf-test/

CHANGELOG.md

@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## TBD
+
+- [[#91](https://github.com/nf-core/scrnaseq/issues/91)] - Change from pytests to nf-test
+
 ## v2.5.1
 
 - Fix that cellranger workflow couldn't be run and enable CI for this workflow ([#288](https://github.com/nf-core/scrnaseq/pull/288)).

nf-test.config

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

tests/main_pipeline_alevin.test

@@ -0,0 +1,67 @@
+nextflow_pipeline {
+
+ name "Test Workflow main.nf"
+ script "main.nf"
+
+ test("test-dataset_alevin_aligner") {
+
+ when {
+ // the rest is taken from shared config
+ params {
+ aligner = 'alevin'
+ outdir = "${outputDir}/results_alevin"
+
+ // Limit resources so that this can run on GitHub Actions -- for some reason it had not been taken from shared config
+ max_cpus = 2
+ max_memory = '6.GB'
+ max_time = '6.h'
+ }
+ }
+
+ then {
+
+ assertAll(
+
+ //
+ // General assertions
+ //
+
+ // Did it finish successfully?
+ {assert workflow.success},
+
+ // How many tasks were executed?
+ {assert workflow.trace.tasks().size() == 16},
+
+ // How many results were produced?
+ {assert path("${outputDir}/results_alevin").list().size() == 5},
+ {assert path("${outputDir}/results_alevin/alevin").list().size() == 4},
+ {assert path("${outputDir}/results_alevin/alevin/mtx_conversions").list().size() == 4},
+ {assert path("${outputDir}/results_alevin/alevinqc").list().size() == 2},
+ {assert path("${outputDir}/results_alevin/fastqc").list().size() == 12},
+ {assert path("${outputDir}/results_alevin/multiqc").list().size() == 3},
+
+ //
+ // Check if files were produced
+ //
+ {assert new File( "${outputDir}/results_alevin/alevin/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ).exists()},
+ {assert new File( "${outputDir}/results_alevin/alevin/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ).exists()},
+
+ //
+ // Check if files are the same
+ //
+ {assert snapshot(
+ workflow,
+ path( "${outputDir}/results_alevin/alevin/Sample_X_alevin_results/af_quant/alevin/quants_mat_cols.txt" ),
+ path( "${outputDir}/results_alevin/alevin/Sample_X_alevin_results/af_quant/alevin/quants_mat.mtx" ),
+ path( "${outputDir}/results_alevin/alevin/Sample_X_alevin_results/af_quant/alevin/quants_mat_rows.txt" ),
+ path( "${outputDir}/results_alevin/alevin/Sample_Y_alevin_results/af_quant/alevin/quants_mat_cols.txt" ),
+ path( "${outputDir}/results_alevin/alevin/Sample_Y_alevin_results/af_quant/alevin/quants_mat.mtx" ),
+ path( "${outputDir}/results_alevin/alevin/Sample_Y_alevin_results/af_quant/alevin/quants_mat_rows.txt" )
+ ).match()}
+
+ ) // end of assertAll()
+
+ }
+ }
+
+}

tests/main_pipeline_alevin.test.snap

@@ -0,0 +1,32 @@
+{
+ "test-dataset_alevin_aligner": {
+ "content": [
+ {
+ "stderr": [
+
+ ],
+ "errorReport": "",
+ "exitStatus": 0,
+ "failed": false,
+ "stdout": [
+
+ ],
+ "errorMessage": "",
+ "trace": {
+ "tasksFailed": 0,
+ "tasksCount": 16,
+ "tasksSucceeded": 16
+ },
+ "name": "workflow",
+ "success": true
+ },
+ "quants_mat_cols.txt:md5,e9868982c17a330392e38c2a5933cf97",
+ "quants_mat.mtx:md5,b8aa7b3c488fd8923de50a3621d4991f",
+ "quants_mat_rows.txt:md5,6227df5a13127b71c71fb18cd8574857",
+ "quants_mat_cols.txt:md5,e9868982c17a330392e38c2a5933cf97",
+ "quants_mat.mtx:md5,54cd12666016adce94c025b2e07f4b02",
+ "quants_mat_rows.txt:md5,6b458a7777260ba90eccbe7919df934b"
+ ],
+ "timestamp": "2024-01-19T10:28:35.652763852"
+ }
+}

tests/main_pipeline_cellranger.test

@@ -0,0 +1,75 @@
+nextflow_pipeline {
+
+ name "Test Workflow main.nf"
+ script "main.nf"
+
+ test("test-dataset_cellranger_aligner") {
+
+ when {
+ // the rest is taken from shared config
+ params {
+ aligner = 'cellranger'
+ outdir = "${outputDir}/results_cellranger"
+
+ // Limit resources so that this can run on GitHub Actions -- for some reason it had not been taken from shared config
+ max_cpus = 2
+ max_memory = '6.GB'
+ max_time = '6.h'
+ }
+ }
+
+ then {
+
+ assertAll(
+
+ //
+ // General assertions
+ //
+
+ // Did it finish successfully?
+ {assert workflow.success},
+
+ // How many tasks were executed?
+ {assert workflow.trace.tasks().size() == 15},
+
+ // How many results were produced?
+ {assert path("${outputDir}/results_cellranger").list().size() == 4},
+ {assert path("${outputDir}/results_cellranger/cellranger").list().size() == 4},
+ {assert path("${outputDir}/results_cellranger/cellranger/mtx_conversions").list().size() == 4},
+ {assert path("${outputDir}/results_cellranger/cellranger/count").list().size() == 3},
+ {assert path("${outputDir}/results_cellranger/fastqc").list().size() == 12},
+ {assert path("${outputDir}/results_cellranger/multiqc").list().size() == 3},
+
+ //
+ // Check if files were produced
+ //
+ {assert new File( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_X/Sample_X_matrix.h5ad" ).exists()},
+ {assert new File( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_Y/Sample_Y_matrix.h5ad" ).exists()},
+
+ //
+ // Check if files are the same
+ //
+ {assert snapshot(
+ workflow,
+ path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/barcodes.tsv.gz" ),
+ path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/features.tsv.gz" ),
+ path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/filtered_feature_bc_matrix/matrix.mtx.gz" ),
+ path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/barcodes.tsv.gz" ),
+ path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/features.tsv.gz" ),
+ path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/filtered_feature_bc_matrix/matrix.mtx.gz" ),
+ path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/barcodes.tsv.gz" ),
+ path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/features.tsv.gz" ),
+ path( "${outputDir}/results_cellranger/cellranger/count/Sample_X/outs/raw_feature_bc_matrix/matrix.mtx.gz" ),
+ path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/barcodes.tsv.gz" ),
+ path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/features.tsv.gz" ),
+ path( "${outputDir}/results_cellranger/cellranger/count/Sample_Y/outs/raw_feature_bc_matrix/matrix.mtx.gz" ),
+ path( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_X/Sample_X_matrix.rds" ),
+ path( "${outputDir}/results_cellranger/cellranger/mtx_conversions/Sample_Y/Sample_Y_matrix.rds" )
+ ).match()}
+
+ ) // end of assertAll()
+
+ }
+ }
+
+}

tests/main_pipeline_cellranger.test.snap

@@ -0,0 +1,40 @@
+{
+ "test-dataset_cellranger_aligner": {
+ "content": [
+ {
+ "stderr": [
+
+ ],
+ "errorReport": "",
+ "exitStatus": 0,
+ "failed": false,
+ "stdout": [
+
+ ],
+ "errorMessage": "",
+ "trace": {
+ "tasksFailed": 0,
+ "tasksCount": 15,
+ "tasksSucceeded": 15
+ },
+ "name": "workflow",
+ "success": true
+ },
+ "barcodes.tsv.gz:md5,fe6e51564b4405b37ca8604a844b1f2e",
+ "features.tsv.gz:md5,99e453cb1443a3e43e99405184e51a5e",
+ "matrix.mtx.gz:md5,79471f700ec5bab852a960f0d1537705",
+ "barcodes.tsv.gz:md5,77afe9a76631fc7b44236d3962a55aa5",
+ "features.tsv.gz:md5,99e453cb1443a3e43e99405184e51a5e",
+ "matrix.mtx.gz:md5,e224aa759250fa5730dc069bce9be253",
+ "barcodes.tsv.gz:md5,85da6b6e0c78dfe81af8c07c2017ab5e",
+ "features.tsv.gz:md5,99e453cb1443a3e43e99405184e51a5e",
+ "matrix.mtx.gz:md5,1bc71041a425bfcee38472bfec5997f8",
+ "barcodes.tsv.gz:md5,081f72b5252ccaf5ffd535ffbd235c4c",
+ "features.tsv.gz:md5,99e453cb1443a3e43e99405184e51a5e",
+ "matrix.mtx.gz:md5,a4db04e43e650accc96361a287126a6b",
+ "Sample_X_matrix.rds:md5,f9191ba575a3ab79ada4807715f18573",
+ "Sample_Y_matrix.rds:md5,7be3f7b29d668dcf7e951b9f4d371a5e"
+ ],
+ "timestamp": "2024-01-22T15:19:20.134275449"
+ }
+}