Specify 72 GB memory for kraken2 #75
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| on: | |
| pull_request: | |
| branches: | |
| - master | |
| name: master Pull Request | |
| jobs: | |
| prepare_caches: | |
| name: Prepare caches | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: create artifacts dir to save test logs | |
| run: mkdir -p artifacts | |
| - name: cache miniconda3 | |
| id: cache-miniconda3 | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| /opt/miniconda3 | |
| /home/runner/.bashrc | |
| key: miniconda3-v1 | |
| - name: install Conda | |
| if: steps.cache-miniconda3.outputs.cache-hit != 'true' | |
| run: bash .github/scripts/install_conda.sh | |
| - name: cache nextflow | |
| id: cache-nextflow | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| /home/runner/bin/nextflow | |
| /home/runner/.nextflow | |
| key: nextflow-v2 | |
| - name: install Nextflow | |
| if: steps.cache-nextflow.outputs.cache-hit != 'true' | |
| run: bash .github/scripts/install_nextflow.sh | |
| - name: cache conda environments | |
| id: cache-conda-envs | |
| uses: actions/cache@v2 | |
| with: | |
| path: /home/runner/.conda/envs | |
| key: conda-envs-v2 | |
| - name: Set up conda cache environment | |
| if: steps.cache-conda-envs.outputs.cache-hit != 'true' | |
| run: bash .github/scripts/set_up_conda_cache.sh | |
| - name: cache hg38_chr22 | |
| id: cache-hg38-chr22 | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| /home/runner/data/chr22.fa* | |
| key: hg38-chr22-v1 | |
| - name: download hg38 chr22 | |
| if: steps.cache-hg38-chr22.outputs.cache-hit != 'true' | |
| run: bash .github/scripts/download_hg38_chr22.sh | |
| - name: cache kraken2/bracken db | |
| id: cache-kraken2-bracken-db | |
| uses: actions/cache@v2 | |
| with: | |
| path: /home/runner/data/kraken2_bracken_db | |
| key: kraken2_bracken_db-v3 | |
| - name: create kraken2/bracken db | |
| if: steps.cache-kraken2-bracken-db.outputs.cache-hit != 'true' | |
| run: bash .github/scripts/create_kraken2_and_bracken_database.sh | |
| - uses: actions/upload-artifact@v1 | |
| if: always() | |
| with: | |
| name: cache_artifacts | |
| path: artifacts | |
| test: | |
| 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: load cache miniconda3 | |
| id: cache-miniconda3 | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| /opt/miniconda3 | |
| /home/runner/.bashrc | |
| key: miniconda3-v1 | |
| - name: load cache nextflow | |
| id: cache-nextflow | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| /home/runner/bin/nextflow | |
| /home/runner/.nextflow | |
| key: nextflow-v2 | |
| - name: load cache conda environments | |
| id: cache-conda-envs | |
| uses: actions/cache@v2 | |
| with: | |
| path: /home/runner/.conda/envs | |
| key: conda-envs-v2 | |
| - name: load cache hg38 chr22 | |
| id: cache-hg38-chr22 | |
| uses: actions/cache@v2 | |
| with: | |
| path: /home/runner/data/chr22.fa* | |
| key: hg38-chr22-v1 | |
| - name: load cache kraken2/bracken db | |
| id: cache-kraken2-bracken-db | |
| uses: actions/cache@v2 | |
| with: | |
| path: /home/runner/data/kraken2_bracken_db | |
| key: kraken2_bracken_db-v3 | |
| - name: test pipeline | |
| run: bash .github/scripts/test_pipeline.sh | |
| - uses: actions/upload-artifact@v1 | |
| if: always() | |
| with: | |
| name: test_artifacts | |
| path: artifacts |