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 check_nextflow_config: runs-on: ubuntu-latest name: Check if nextflow config runs in repository root steps: - uses: actions/checkout@v1 - name: Install Nextflow run: | wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ - run: nextflow config -show-profiles ${GITHUB_WORKSPACE} profile_test: runs-on: ubuntu-latest name: Run ${{ matrix.profile }} profile needs: test_all_profiles strategy: matrix: profile: - "abims" - "adcra" - "alice" - "aws_tower" - "awsbatch" - "azurebatch" - "bi" - "bigpurple" - "binac" - "biohpc_gen" - "cambridge" - "leicester" - "cbe" - "ccga_dx" - "ccga_med" - "cedars" - "cfc" - "cfc_dev" - "cheaha" - "computerome" - "crick" - "crukmi" - "denbi_qbic" - "ebc" - "eddie" - "eva" - "fgcz" - "genotoul" - "genouest" - "gis" - "google" - "hasta" - "hebbe" - "hki" - "icr_davros" - "ifb_core" - "imperial" - "jax" - "lugh" - "marvin" - "medair" - "mjolnir_globe" - "maestro" - "mpcdf" - "munin" - "nu_genomics" - "nihbiowulf" - "oist" - "pasteur" - "phoenix" - "prince" - "rosalind" - "sage" - "sahmri" - "sanger" - "sbc_sharc" - "seg_globe" - "uct_hpc" - "unibe_ibu" - "uppmax" - "utd_ganymede" - "utd_sysbio" - "uzh" - "vai" - "vsc_ugent" 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 -profile ${{ matrix.profile }}