main.yml

name: Configs tests

on: [pull_request, push]
jobs:
  test_all_profiles:
    runs-on: ubuntu-latest
    name: Check if all profiles are tested
    steps:
      - uses: actions/checkout@v1
      - name: Check whether profiles are all tested
        run: |
          python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml
  profile_test:
    runs-on: ubuntu-latest
    name: Run ${{ matrix.profile }} profile
    needs: test_all_profiles
    strategy:
        matrix:
          profile: ['awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'kraken', 'mpcdf', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
    steps:
      - uses: actions/checkout@v1
      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
      - name: Check ${{ matrix.profile }} profile
        env:
          SCRATCH: '~'
          NXF_GLOBAL_CONFIG: awsbatch.config
        run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }}