ci.yml

# 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 }}"
  cancel-in-progress: true

jobs:
  test:
    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: ["alevin", "cellranger", "kallisto", "star"]

    steps:
      - name: Disk space cleanup
        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

      - name: Check out pipeline code
        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v1
        with:
          version: "${{ matrix.NXF_VER }}"

      - name: Run pipeline with test data
        # TODO nf-core: You can customise CI pipeline run tests as required
        # 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: |
          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