Add github actions testing pipeline #7
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| on: | |
| pull_request: | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| name: Pull Request | |
| jobs: | |
| test: | |
| name: Run tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: create artifacts dir to save test logs | |
| run: mkdir artifacts | |
| - name: Install Miniconda | |
| run: bash .github/scripts/install_conda.sh | |
| - name: Install Nextflow | |
| run: bash .github/scripts/install_nextflow.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: conda init && source ~/.bashrc && conda activate art && bash ./github/scripts/simulate_reads.sh | |
| - name: Upload Artifacts | |
| uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: test_artifacts | |
| path: artifacts |