Explore consensus cell types in osteosarcoma samples #41
Workflow file for this run
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| # This is a workflow to run the cell-type-consensus 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-consensus analysis module | |
| env: | |
| MODULE_PATH: analyses/cell-type-consensus | |
| AWS_DEFAULT_REGION: us-east-2 | |
| concurrency: | |
| # only one run per branch at a time | |
| group: "run_cell-type-consensus_${{ github.ref }}" | |
| cancel-in-progress: true | |
| on: | |
| workflow_dispatch: | |
| workflow_call: | |
| pull_request: | |
| branches: | |
| - main | |
| paths: | |
| - analyses/cell-type-consensus/** | |
| - "!analyses/cell-type-consensus/Dockerfile" | |
| - "!analyses/cell-type-consensus/.dockerignore" | |
| - .github/workflows/run_cell-type-consensus.yml | |
| jobs: | |
| run-module: | |
| if: github.repository_owner == 'AlexsLemonade' | |
| runs-on: ubuntu-latest | |
| container: public.ecr.aws/openscpca/cell-type-consensus:latest | |
| steps: | |
| - name: Install aws-cli | |
| run: | | |
| curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" | |
| unzip -q awscliv2.zip | |
| ./aws/install | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| # Update this step as needed to download the desired data | |
| # regular single cell, multiplexed, and cell line projects for testing | |
| - name: Download test data | |
| run: ./download-data.py --test-data --format SCE --project SCPCP000001,SCPCP000009,SCPCP0000024 | |
| - name: Run analysis module | |
| run: | | |
| projects=$(basename -a data/current/SCPCP*) | |
| cd ${MODULE_PATH} | |
| for project in $projects; do | |
| ./assign-consensus-celltypes.sh $project | |
| done |