ci.yml

name: CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
  push:
    branches:
      - dev
      - 260-improve-ci
  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
    # Only run on push if this is in the main repository
    if: "${{ github.event_name == 'push' && github.repository == 'genomic-medicine-sweden/jasen' }}"
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "23.10.1"
        parameters:
          - "-profile staphylococcus_aureus"
          - "-profile mycobacterium_tuberculosis"
          - "-profile klebsiella_pneumoniae"
          - "-profile escherichia_coli"
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v3

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v1
        with:
          version: "${{ matrix.NXF_VER }}"

      - name: Run pipeline with test data
        run: |
          nextflow run ${GITHUB_WORKSPACE}/main.nf ${{ matrix.parameters }} -config configs/nextflow.testrun.config --csv assets/test_data/samplelist.testrun.csv