Add initial evaluation notebook to metacells module #7
Workflow file for this run
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| # This is a workflow to run the metacells module | |
| # | |
| # Analysis modules are run based on three triggers: | |
| # - Manual trigger | |
| # - On pull requests where code in the module has changed | |
| # - As a reusable workflow called from a separate workflow which periodically runs all modules | |
| # | |
| # At initialization, only the manual trigger is active | |
| name: Run metacells analysis module | |
| env: | |
| MODULE_PATH: analyses/metacells | |
| AWS_DEFAULT_REGION: us-east-2 | |
| concurrency: | |
| # only one run per branch at a time | |
| group: "run_metacells_${{ github.ref }}" | |
| cancel-in-progress: true | |
| on: | |
| workflow_dispatch: | |
| workflow_call: | |
| pull_request: | |
| branches: | |
| - main | |
| paths: | |
| - analyses/metacells/** | |
| - "!analyses/metacells/Dockerfile" | |
| - "!analyses/metacells/.dockerignore" | |
| - .github/workflows/run_metacells.yml | |
| jobs: | |
| run-module: | |
| if: github.repository_owner == 'AlexsLemonade' | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Set up conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| - name: Install and activate locked conda environment | |
| run: | | |
| conda install conda-lock | |
| conda-lock install --name openscpca-metacells ${MODULE_PATH}/conda-lock.yml | |
| conda activate openscpca-metacells | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 4.4.0 | |
| use-public-rspm: true | |
| - name: Set up pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Set up renv | |
| uses: r-lib/actions/setup-renv@v2 | |
| with: | |
| working-directory: ${{ env.MODULE_PATH }} | |
| # Downloading just one sample for initial testing | |
| - name: Download test data | |
| run: ./download-data.py --test-data --format AnnData --sample SCPCS000001 | |
| - name: Run analysis module | |
| run: | | |
| cd ${MODULE_PATH} | |
| # run module script here | |
| bash run-metacells.sh |