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
  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: 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 == 'sanger-tol/curationpretext') }}"
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        NXF_VER:
          - "24.04.0"
          - "latest-everything"

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

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

      - name: Download test data
        # Download A fungal test data set that is full enough to show some real output.
        run: |
          curl https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData.tar.gz | tar xzf -

      - name: Install nf-test
        uses: nf-core/setup-nf-test@v1

      # Test the component
      - name: Run nf-test
        run: |
          nf-test test \
            --profile="docker" \
            --debug \
            --verbose

      # - name: Run ALL_FILES pipeline with test data
      #   # Remember that you can parallelise this by using strategy.matrix
      #   run: |
      #     nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
