diff --git a/.github/workflows/nextflow_CI.yml b/.github/workflows/nextflow_CI.yml index f775bf1..90efd18 100644 --- a/.github/workflows/nextflow_CI.yml +++ b/.github/workflows/nextflow_CI.yml @@ -38,6 +38,20 @@ jobs: - name: Run pipeline test (reference) run: | nextflow run main.nf -profile docker --prefix "covidmvp-$(date +%Y-%m-%d)" --end_date $(date +%Y-%m-%d) -params-file covidmvp_clinical_params.yaml + test_sarscov2_timeseries: + name: Run pipeline test (user) + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + + - name: Install Nextflow + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + + - name: Run pipeline test (timeseries) + run: | + nextflow run main.nf -profile docker --prefix "covidmvp-timeseries-$(date +%Y-%m-%d)" -params-file covidmvp_timeseries_params.yaml check_success: name: Check if all tests passed