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
  NFT_VER: "0.9.0"
  NFT_WORKDIR: "~"
  NFT_DIFF: "pdiff"
  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity

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:
          - "24.04.2"
          - "latest-everything"
        profile: ["alevin", "cellranger", "cellrangermulti", "kallisto", "star"]

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

      - name: Check out pipeline code
        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

      - uses: actions/setup-python@v4
        with:
          python-version: "3.11"
          architecture: "x64"

      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
        with:
          distribution: "temurin"
          java-version: "17"

      - name: Install pdiff to see diff between nf-test snapshots
        run: |
          python -m pip install --upgrade pip
          pip install pdiff

      - uses: nf-core/setup-nextflow@v2
        with:
          version: "${{ matrix.NXF_VER }}"

      - uses: nf-core/setup-nf-test@v1
        with:
          version: ${{ env.NFT_VER }}

      - name: Run nf-test
        run: |
          nf-test test \
            --ci \
            --junitxml=test.xml \
            tests/main_pipeline_${{ matrix.profile }}.nf.test

      - 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