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', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', '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 }}