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:
      - main
  pull_request:
  release:
    types: [published]

env:
  NXF_ANSI_LOG: false

jobs:
  #   test-stub:
  #     name: Run pipeline with stubs
  #     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'beiko-lab/arete') }}"
  #     runs-on: ubuntu-latest
  #     strategy:
  #       matrix:
  #         NXF_VER:
  #           - "latest-everything"
  #     steps:
  #       - name: Check out pipeline code
  #         uses: actions/checkout@v2

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

  #       - name: Run pipeline stub-run
  #         run: |
  #           nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub-run --outdir ./stub_results

  test:
    name: Run pipeline with test data
    runs-on: ubuntu-latest
    strategy:
      matrix:
        profile: ["docker", "singularity"]
        NXF_VER:
          - "latest-everything"
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v2

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

      - name: Set up Singularity
        if: matrix.profile == 'singularity'
        uses: eWaterCycle/setup-singularity@v5
        with:
          singularity-version: 3.7.1

      - name: Run pipeline with test data
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test,${{ matrix.profile }} --outdir ./results