ci.yml

name: nf-core CI

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
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        NXF_VER:
          - "22.10.1"
          - "latest-everything"
        short_aligner:
          - bwamem2
          - minimap2
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v3

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

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