updated mpox test_data #23
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| name: Nextflow CI | |
| on: | |
| push: | |
| branches: | |
| - development | |
| pull_request: | |
| branches: | |
| - master | |
| jobs: | |
| test_sarscov2_user: | |
| name: Run pipeline test (sarscov2_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 (sarscov2_user) | |
| run: | | |
| nextflow run main.nf -profile docker --prefix "covidmvp-user-$(date +%Y-%m-%d)" -params-file covidmvp_user_params.yaml | |
| test_sarscov2_reference: | |
| name: Run pipeline test (sarscov2_reference) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline test (sarscov2_reference) | |
| run: | | |
| nextflow run main.nf -profile docker --prefix "covidmvp-clinical-$(date +%Y-%m-%d)" --end_date $(date +%Y-%m-%d) -params-file covidmvp_clinical_params.yaml | |
| test_sarscov2_timeseries: | |
| name: Run pipeline test (sarscov2_timeseries) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline test (sarscov2_timeseries) | |
| run: | | |
| nextflow run main.nf -profile docker --prefix "covidmvp-timeseries-$(date +%Y-%m-%d)" -params-file covidmvp_timeseries_params.yaml | |
| test_sarscov2_wastewater: | |
| name: Run pipeline test (sarscov2_wastewater) | |
| 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 (sarscov2_wastewater) | |
| run: | | |
| nextflow run main.nf -profile docker --prefix "covidmvp-wastewater-$(date +%Y-%m-%d)" -params-file covidmvp_wastewater_params.yaml | |
| test_mpox_user: | |
| name: Run pipeline test (mpox_user) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline test (mpox_user) | |
| run: | | |
| nextflow run main.nf -profile docker --prefix "poxmvp-user-$(date +%Y-%m-%d)" -params-file poxmvp_user_params.yaml | |
| test_mpox_reference: | |
| name: Run pipeline test (mpox_reference) | |
| 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 (mpox_reference) | |
| run: | | |
| nextflow run main.nf -profile docker --prefix "poxmvp-reference-$(date +%Y-%m-%d)" -params-file poxmvp_clinical_params.yaml | |
| check_success: | |
| name: Check if all tests passed | |
| needs: | |
| [ | |
| test_sarscov2_user, | |
| test_sarscov2_reference, | |
| test_sarscov2_timeseries, | |
| test_sarscov2_wastewater, | |
| test_mpox_reference, | |
| test_mpox_user, | |
| ] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check job status | |
| if: ${{ failure() }} | |
| run: exit 1 |