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 }}