fix: distinguish soft and hard AF filter #17
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| # Testing for pipeline python wrapper and scripts used inside rules | |
| name: Singularity e2e test | |
| on: [pull_request] | |
| env: | |
| KRAKEN_DEFAULT_DB: /mnt/kraken-database | |
| jobs: | |
| singularity_end_to_end: | |
| runs-on: ${{ matrix.config.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: ubuntu-latest} | |
| name: Singularity Juno_mapping pipeline ${{ matrix.config.os }} | |
| steps: | |
| - name: check space 1 | |
| shell: bash -l {0} | |
| run: | | |
| sudo chmod -R 777 /mnt | |
| echo "Checking space: ." | |
| df -h . | |
| echo "Checking space: /mnt" | |
| df -h /mnt | |
| - uses: actions/checkout@v4 | |
| - uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.8.3 | |
| - name: Install Conda environment with Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| generate-run-shell: false # see https://github.com/mamba-org/setup-micromamba/issues/130 | |
| cache-downloads: true | |
| environment-file: envs/juno_mapping.yaml | |
| environment-path: /mnt/juno_mapping | |
| - name: Cache minikraken | |
| id: cache-minikraken | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.KRAKEN_DEFAULT_DB }} | |
| key: minikraken-${{ runner.os }} | |
| - name: Download k2 database | |
| if: steps.cache-minikraken.outputs.cache-hit != 'true' | |
| run: | | |
| mkdir -pv ${{ env.KRAKEN_DEFAULT_DB }} | |
| cd ${{ env.KRAKEN_DEFAULT_DB }} | |
| curl -k https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20220908.tar.gz > k2_viral_20220908.tar.gz | |
| tar zxvf k2_viral_20220908.tar.gz | |
| ls -lh | |
| rm k2_viral_20220908.tar.gz | |
| - name: Conda list | |
| shell: bash -l {0} | |
| run: conda list | |
| - name: check space 2 | |
| shell: bash -l {0} | |
| run: | | |
| which singularity | |
| singularity --version | |
| df -h . | |
| if [ -d /home/runner ]; then | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| fi | |
| echo "Checking space: ." | |
| df -h . | |
| echo "Checking space: /mnt" | |
| df -h /mnt | |
| which singularity | |
| singularity --version | |
| - name: Test juno_mapping pipeline using singularity. | |
| shell: bash -l {0} | |
| run: pytest -v tests/test_pipeline_singularity.py | |
| - name: Test the juno_mapping wrapper | |
| shell: bash -l {0} | |
| run: pytest -v tests/test_juno_mapping.py | |
| - name: check space 3 | |
| if: always() | |
| shell: bash -l {0} | |
| run: | | |
| echo "Checking space: ." | |
| df -h . | |
| echo "Checking space: /mnt" | |
| df -h /mnt |