ci.yml

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:
    branches:
      - dev
  pull_request:
  release:
    types: [published]

env:
  NXF_ANSI_LOG: false

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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/scrnaseq') }}"
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "23.04.0"
          - "latest-everything"
        profile: [
            "test,docker --aligner alevin",
            "test,docker --aligner kallisto",
            "test,docker --aligner star",
            "test,docker --aligner cellranger",
            # "test,docker --aligner cellrangerarc", // this currently lacks a suitable test profile, see issue https://github.com/nf-core/scrnaseq/issues/290
            # "test,docker --aligner universc", // this is broken, see issue https://github.com/nf-core/scrnaseq/issues/289
          ]
    steps:
      - name: Free some space
        run: |
          sudo rm -rf /usr/share/dotnet
          sudo rm -rf /opt/ghc
          sudo rm -rf "/usr/local/share/boost"
          sudo rm -rf "$AGENT_TOOLSDIRECTORY"
      - name: Check out pipeline code
        uses: actions/checkout@v4

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v1
        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
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }} --outdir ./results