Handle case where segment is missing while plotting scaffold (#33) #46
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| on: | |
| pull_request: | |
| branches: | |
| - main | |
| push: | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| name: Consistency Check | |
| jobs: | |
| test: | |
| name: Check Consistency vs. KevinKuchinski/FluViewer | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python_version: | |
| - "3.8" | |
| - "3.9" | |
| - "3.10" | |
| - "3.11" | |
| - "3.12" | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: Create Artifacts Directory | |
| run: mkdir artifacts | |
| - name: Install Conda | |
| run: bash .github/scripts/install_conda.sh | |
| - name: Create ART Read-Simulation Environment | |
| run: bash .github/scripts/create_art_environment.sh | |
| - name: Download Assemblies | |
| run: bash .github/scripts/download_assemblies.sh | |
| - name: Simulate Reads | |
| run: bash .github/scripts/simulate_reads.sh | |
| - name: Create SRA-Tools Environment | |
| run: bash .github/scripts/create_sra-tools_environment.sh | |
| - name: Download SRA Reads | |
| run: bash .github/scripts/download_sra_reads.sh | |
| - name: Download FluViewer db | |
| run: bash .github/scripts/download_fluviewer_db.sh | |
| - name: Install KevinKuchinski/FluViewer | |
| run: bash .github/scripts/install_fluviewer_kkuchinski.sh | |
| - name: Run analysis with KevinKuchinski/FluViewer | |
| run: bash .github/scripts/run_analysis_upstream.sh | |
| - name: Install BCCDC-PHL/FluViewer | |
| run: bash .github/scripts/install_fluviewer_bccdc-phl.sh | |
| - name: Run analysis with BCCDC-PHL/FluViewer | |
| run: bash .github/scripts/run_analysis_origin.sh | |
| - name: Check Outputs | |
| run: bash .github/scripts/check_outputs.sh | |
| - name: Prepare Artifacts | |
| if: always() | |
| run: bash .github/scripts/prepare_artifacts.sh | |
| - name: Upload Artifacts | |
| uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: artifacts-BCCDC-PHL-FluViewer-python-v${{ matrix.python_version }}-${{ github.run_id }}.${{ github.run_attempt }} | |
| path: artifacts |