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push-stub-run.yml
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name: Nextflow Stub Runs
on:
push:
branches: [ main ]
pull_request:
branches: [ '**' ]
jobs:
stub-run:
runs-on: ubuntu-latest
strategy:
matrix:
config: [
'test-diann.config',
'test-encyclopedia-narrow-gpf.config',
'test-encyclopedia-wide-only.config',
'test-diann-pdc.config',
'test-msconvert-only-pdc.config',
'test-msconvert-only-local.config'
]
steps:
- name: Checkout repository
uses: actions/checkout@v2
- name: Run (${{ matrix.config }})
run: |
echo "Installing Nextflow:"
export NXF_VER=24.04.4 # Specify nextflow version. Currently there is a bug in 24.10.0
curl -s https://get.nextflow.io | bash
chmod +x nextflow
echo "Running Nextflow stub with config: ${{ matrix.config }}"
./nextflow run . -stub-run -c test-resources/${{ matrix.config }}