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
    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'Plant-Food-Research-Open/genepal') }}"
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "23.04.0"
        TEST_PARAMS:
          - minimal
          - short
          - nonmasked
          - stub
        OPTION_STUB:
          - "-stub"

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

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

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

      - name: Run pipeline with test data
        run: |
          nextflow run \
            ${GITHUB_WORKSPACE} \
            -profile docker \
            -params-file \
            ./tests/${{ matrix.TEST_PARAMS }}/params.json \
            ${{ matrix.OPTION_STUB }} \
            --outdir ./results