nf-configs/.github/workflows/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

  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'
            - 'alice'
            - 'aws_tower'
            - 'awsbatch'
            - 'azurebatch'
            - 'bi'
            - 'bigpurple'
            - 'binac'
            - 'biohpc_gen'
            - 'cambridge'
            - 'leicester'
            - 'cbe'
            - 'ccga_dx'
            - 'ccga_med'
            - 'cfc'
            - 'cfc_dev'
            - 'cheaha'
            - 'computerome'
            - 'crick'
            - 'denbi_qbic'
            - 'ebc'
            - 'eddie'
            - 'eva'
            - 'fgcz'
            - 'genotoul'
            - 'genouest'
            - 'gis'
            - 'google'
            - 'hasta'
            - 'hebbe'
            - 'icr_davros'
            - 'ifb_core'
            - 'imperial'
            - 'jax'
            - 'lugh'
            - 'marvin'
            - 'maestro'
            - 'mpcdf'
            - 'munin'
            - 'nu_genomics'
            - 'nihbiowulf'
            - 'oist'
            - 'pasteur'
            - 'phoenix'
            - 'prince'
            - 'rosalind'
            - 'sahmri'
            - 'sanger'
            - 'seg_globe'
            - 'uct_hpc'
            - 'unibe_ibu'
            - 'uppmax'
            - 'utd_ganymede'
            - 'utd_sysbio'
            - 'uzh'
            - 'vai'
    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 }}