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

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/hlatyping') }}"
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "21.10.3"
          - "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 with test data
        # For example: adding multiple test runs with different parameters
        # Remember that you can parallelise this by using strategy.matrix
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
  profile:
    name: Run profile tests
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/hlatyping') }}
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "21.10.3"
          - "latest-everything"
        tests: ["test_fastq", "test_rna", "test_dna_rna"]
    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 with profile ${{ matrix.tests }}
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --outdir ./results