cell type/tumor annotation for ETP T-ALL (SCPCP000003) #3
Workflow file for this run
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| # This is a workflow to run the cell-type-ETP-ALL-03 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 cell-type-ETP-ALL-03 analysis module | |
| env: | |
| MODULE_PATH: analyses/cell-type-ETP-ALL-03 | |
| AWS_DEFAULT_REGION: us-east-2 | |
| concurrency: | |
| # only one run per branch at a time | |
| group: "run_cell-type-ETP-ALL-03_${{ github.ref }}" | |
| cancel-in-progress: true | |
| on: | |
| workflow_dispatch: | |
| workflow_call: | |
| pull_request: | |
| branches: | |
| - main | |
| paths: | |
| - analyses/cell-type-ETP-ALL-03/** | |
| - "!analyses/cell-type-ETP-ALL-03/Dockerfile" | |
| - "!analyses/cell-type-ETP-ALL-03/.dockerignore" | |
| - .github/workflows/run_cell-type-ETP-ALL-03.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 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: Install system dependencies | |
| run: | | |
| sudo apt-get install -y libcurl4-openssl-dev \ | |
| libhdf5-dev \ | |
| libglpk40 \ | |
| libxml2-dev \ | |
| libfontconfig1-dev \ | |
| libharfbuzz-dev \ | |
| libfribidi-dev \ | |
| libtiff5-dev | |
| - name: Set up renv | |
| uses: r-lib/actions/setup-renv@v2 | |
| with: | |
| working-directory: ${{ env.MODULE_PATH }} | |
| - name: Set up conda | |
| # Note that this creates and activates an environment named 'test' by default | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| - name: Install conda-lock and activate locked conda environment | |
| run: | | |
| conda install conda-lock | |
| conda-lock install --name openscpca-cell-type-ETP-ALL-03 ${MODULE_PATH}/conda-lock.yml | |
| # Update this step as needed to download the desired data | |
| - name: Download test data | |
| run: | | |
| ./download-data.py --projects SCPCP000003 --test-data --format SCE | |
| ./download-results.py --projects SCPCP000003 --test-data --modules doublet-detection | |
| - name: Run analysis module | |
| run: | | |
| cd ${MODULE_PATH} | |
| # run module script(s) here | |
| Rscript scripts/00-01_processing_rds.R | |
| Rscript scripts/02-03_annotation.R | |
| Rscript scripts/multipanel_plot.R |