Specify 72 GB memory for kraken2 #4
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| on: | |
| pull_request: | |
| branches: | |
| - master | |
| name: Tests | |
| jobs: | |
| test: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| nextflow_version: ["21.04.3", "23.10.1", "24.04.3"] | |
| name: Run tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: Create artifacts dir to save test logs | |
| run: mkdir -p artifacts | |
| - name: Install Conda | |
| run: bash .github/scripts/install_conda.sh | |
| - name: Install Nextflow | |
| env: | |
| NXF_VER: ${{ matrix.nextflow_version }} | |
| run: bash .github/scripts/install_nextflow.sh | |
| - name: Set up conda cache environment | |
| run: bash .github/scripts/set_up_conda_cache.sh | |
| - name: Download hg38 chr22 | |
| run: bash .github/scripts/download_hg38_chr22.sh | |
| - name: Create kraken2/bracken db | |
| run: bash .github/scripts/create_kraken2_and_bracken_database.sh | |
| - name: Run Pipeline | |
| env: | |
| NXF_VER: ${{ matrix.nextflow_version }} | |
| run: bash .github/scripts/test_pipeline.sh | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: artifacts-BCCDC-PHL-dehost-and-verify-illumina-nextflow-v${{ matrix.nextflow_version }}-${{ github.run_id }}.${{ github.run_attempt }} | |
| path: artifacts |