Adapt Azimuth code for Wilms label transfer #246
Workflow file for this run
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| # This is a workflow to run the cell-type-wilms-tumor-06 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-wilms-tumor-06 analysis module | |
| env: | |
| MODULE_PATH: analyses/cell-type-wilms-tumor-06 | |
| AWS_DEFAULT_REGION: us-east-2 | |
| concurrency: | |
| # only one run per branch at a time | |
| group: "run_cell-type-wilms-tumor-06_${{ github.ref }}" | |
| cancel-in-progress: true | |
| on: | |
| workflow_dispatch: | |
| workflow_call: | |
| pull_request: | |
| branches: | |
| - main | |
| - feature/* | |
| paths: | |
| - analyses/cell-type-wilms-tumor-06/** | |
| - "!analyses/cell-type-wilms-tumor-06/Dockerfile" | |
| - "!analyses/cell-type-wilms-tumor-06/.dockerignore" | |
| - .github/workflows/run_cell-type-wilms-tumor-06.yml | |
| jobs: | |
| run-module: | |
| if: github.repository_owner == 'AlexsLemonade' | |
| runs-on: ubuntu-latest | |
| container: public.ecr.aws/openscpca/cell-type-wilms-tumor-06:latest | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Install aws-cli | |
| run: | | |
| curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" | |
| unzip awscliv2.zip | |
| sudo ./aws/install | |
| - name: Download test data | |
| env: | |
| # Use all samples for testing unless this is triggered by a PR, in which case only use a subset of samples for faster testing | |
| # These samples were selected because they are the subset of samples explored when evaluating CNV methods, | |
| # so they must be present to run the module workflow in full. | |
| DOWNLOAD_FLAG: ${{ github.event_name != 'pull_request' && '--projects SCPCP000006' || '--samples SCPCS000179,SCPCS000184,SCPCS000194,SCPCS000205,SCPCS0000208' }} | |
| run: ./download-data.py --test-data --format SCE ${DOWNLOAD_FLAG} | |
| - name: Run analysis module | |
| run: TESTING=1 bash 00_run_workflow.sh | |
| working-directory: ${{ env.MODULE_PATH }} |