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

env:
  NXF_ANSI_LOG: false
  CAPSULE_LOG: none
  NFTEST_VER: "0.7.3"

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/spatialvi') }}"
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        NXF_VER:
          - "23.04.0"
          - "latest-everything"
        test:
          - tests/pipeline/test_spaceranger_ffpe_v1.nf.test
          - tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test
          - tests/pipeline/test_downstream.nf.test
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

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

      # Install nf-test
      - name: Install nf-test
        run: |
          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
          sudo mv nf-test /usr/local/bin/

      # Run nf-test
      - name: Run nf-test
        run: nf-test test --profile=test,docker --tap=test.tap ${{ matrix.test }}

      # If the test fails, output the software_versions.yml using the 'batcat' utility
      - name: Output log on failure
        if: failure()
        run: |
          sudo apt install bat > /dev/null
          batcat --decorations=always --color=always .nf-test/tests/*/output/pipeline_info/software_versions.yml