Snake8 #312
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| name: Combined Workflow | |
| on: | |
| # Runs on pushes targeting the default branch | |
| push: | |
| branches: ["master"] | |
| pull_request: | |
| branches: ["master"] | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| defaults: | |
| run: | |
| shell: bash -el {0} # use default shell | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| build-and-dryrun: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 1 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3.5.2 | |
| # - name: Get current month | |
| # id: date | |
| # run: echo "date=$(date +%Y-%m)" >> "${GITHUB_OUTPUT}" | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: atlasenv.yml | |
| environment-name: atlasenv | |
| # persist on the same month. | |
| cache-environment-key: atlasenv- #${{ steps.date.outputs.date }} | |
| - name: Install atlas | |
| run: | | |
| python -m pip install . --no-deps -vv | |
| - name: Test atlas | |
| run: | | |
| atlas --help | |
| atlas --version | |
| - name: test import modules atlas | |
| run: | | |
| python -c "from atlas import utils" | |
| - name: Dryrun | |
| run: test/dryrun.sh | |
| run-qc-and-assembly: | |
| runs-on: ubuntu-latest | |
| needs: build-and-dryrun | |
| env: | |
| N_THREADS: 2 | |
| MEM: 0.8 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3.5.2 | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: atlasenv.yml | |
| environment-name: atlasenv | |
| cache-environment-key: atlasenv- | |
| - name: Install atlas | |
| run: | | |
| python -m pip install . --no-deps -vv | |
| atlas --help | |
| - name: get example data | |
| id: get-data | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: test_reads.tar.gz | |
| key: example-data | |
| - name: Download test data | |
| if: steps.get-data.outputs.cache-hit != 'true' | |
| run: wget --quiet https://zenodo.org/record/3992790/files/test_reads.tar.gz | |
| - name: cache example data | |
| if: steps.get-data.outputs.cache-hit != 'true' | |
| uses: actions/cache/save@v3 | |
| with: | |
| path: test_reads.tar.gz | |
| key: ${{ steps.get-data.outputs.cache-primary-key }} | |
| - name: extract data | |
| run: | | |
| tar -xzf test_reads.tar.gz | |
| ls -l test_reads | |
| - name: get conda envs | |
| id: get-envs | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: databases | |
| key: conda-envs-assembly | |
| # - name: upack conda envs | |
| # if: steps.get-envs.outputs.cache-hit != 'true' | |
| # run: tar -xzf assembly_conda_envs.tar.gz | |
| - name: Init | |
| run: | | |
| atlas init "test_reads" --threads "$N_THREADS" --working-dir wd | |
| - name: Install dependencies for qc and assembly | |
| if: steps.get-envs.outputs.cache-hit != 'true' | |
| run: atlas run assembly --conda-create-envs-only -w wd | |
| - name: List envs | |
| run: ls -l databases/conda_envs | |
| - name: Store conda envs | |
| if: steps.get-envs.outputs.cache-hit != 'true' | |
| uses: actions/cache/save@v3 | |
| with: | |
| path: databases | |
| key: ${{ steps.get-envs.outputs.cache-primary-key }} | |
| - name: Run QC | |
| run: | | |
| atlas run qc --max-mem $MEM --jobs=$N_THREADS --restart-times=2 --working-dir wd | |
| - name: Test Assembly | |
| run: | | |
| atlas run assembly --max-mem $MEM --jobs=$N_THREADS --restart-times=2 --working-dir wd | |
| - name: Store Logs | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: logs | |
| path: wd/logs | |
| - name: Store Sample Logs | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: sample_logs | |
| path: wd/sample1/logs | |
| - name: Store reports | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: reports | |
| path: wd/reports | |
| - name: Cache working dir | |
| uses: actions/cache/save@v3 | |
| with: | |
| path: wd | |
| key: assembly-working-dir | |
| run-genecatalog: | |
| runs-on: ubuntu-latest | |
| needs: [build-and-dryrun, run-qc-and-assembly] | |
| env: | |
| N_THREADS: 2 | |
| MEM: 3 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3.5.2 | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: atlasenv.yml | |
| environment-name: atlasenv | |
| cache-environment-key: atlasenv- | |
| - name: install atlas | |
| run: | | |
| python -m pip install . --no-deps -vv | |
| atlas --help | |
| - name: get conda envs | |
| id: get-envs | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: databases | |
| key: conda-envs-genecatalog | |
| restore-keys: | | |
| conda-envs-assembly | |
| conda-envs- | |
| - name: Restore working dir | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: wd | |
| key: assembly-working-dir | |
| - name: dryrun assembly shold need nothing to be done | |
| run: | | |
| ls -l wd | |
| ls -l databases/conda_envs | |
| atlas run assembly -w wd -n | |
| - name: test Genecatalog | |
| run: | | |
| atlas run genecatalog --restart-times=2 --working-dir wd --omit-from combine_egg_nogg_annotations combine_dram_genecatalog_annotations | |
| - name: Store Logs | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: logs | |
| path: wd/logs | |
| - name: Store Sample Logs | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: sample_logs | |
| path: wd/sample1/logs | |
| - name: Store conda envs | |
| #if: steps.get-envs.outputs.cache-hit != 'true' | |
| uses: actions/cache/save@v3 | |
| with: | |
| path: databases | |
| key: ${{ steps.get-envs.outputs.cache-primary-key }} | |
| run-binning: | |
| runs-on: ubuntu-latest | |
| needs: [build-and-dryrun, run-qc-and-assembly] | |
| env: | |
| MEM: 0.9 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3.5.2 | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: atlasenv.yml | |
| environment-name: atlasenv | |
| cache-environment-key: atlasenv- | |
| - name: install atlas | |
| run: | | |
| python -m pip install . --no-deps -vv | |
| atlas --help | |
| - name: get conda envs | |
| id: get-envs | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: databases | |
| key: conda-envs-binning | |
| restore-keys: | | |
| conda-envs- | |
| - name: Restore working dir | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: wd | |
| fail-on-cache-miss: true | |
| key: assembly-working-dir | |
| - name: dryrun assembly shold need nothing to be done | |
| run: | | |
| ls -l wd | |
| ls -l databases | |
| ls -l databases/conda_envs | |
| atlas run assembly -w wd -n | |
| - name: test binning | |
| run: | | |
| atlas run binning --restart-times=2 --working-dir wd --omit-from checkm2_download_db --max-mem $MEM &> >(tee wd/logs/atlas_binning.log) | |
| - name: Store Logs | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: logs_binning | |
| path: wd/logs | |
| - name: Store Sample Logs | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: sample_logs_binning | |
| path: wd/sample1/logs | |
| - name: Store conda envs | |
| # if: steps.get-envs.outputs.cache-hit != 'true' | |
| uses: actions/cache/save@v3 | |
| with: | |
| path: databases | |
| key: ${{ steps.get-envs.outputs.cache-primary-key }} | |
| # run-quantify-genomes: | |
| # runs-on: ubuntu-latest | |
| # needs: build-and-dryrun | |
| # steps: | |
| # - name: Checkout | |
| # uses: actions/checkout@v3.5.2 | |
| # - uses: mamba-org/setup-micromamba@v1 | |
| # with: | |
| # environment-file: atlasenv.yml | |
| # environment-name: atlasenv | |
| # cache-environment-key: atlasenv- | |
| # - name: Install atlas | |
| # run: | | |
| # python -m pip install . --no-deps -vv | |
| # atlas --help | |
| # - name: get conda envs | |
| # id: get-envs | |
| # uses: actions/cache/restore@v3 | |
| # with: | |
| # path: databases | |
| # key: conda-envs-assembly | |
| # restore-keys: conda-envs-* |