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nf-configs/.github/workflows/main.yml

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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: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', '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 }}