Add scAdvanced GSEA notebook that uses pseudobulk RMS DE results #692
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Test render notebooks | |
| # Before merging notebooks, check that they render | |
| on: | |
| pull_request: | |
| branches: | |
| - master | |
| paths: | |
| - '**.Rmd' | |
| - '!**-live.Rmd' # don't trigger for live-only changes | |
| - '!**/exercise*.Rmd' # or exercise notebooks | |
| - '!**/setup/**.Rmd' # or setup notebooks | |
| - 'scripts/make-live.R' | |
| - 'scripts/render-live.sh' | |
| jobs: | |
| test-render: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ccdl/training_rstudio:edge | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Load 1Password secrets | |
| uses: 1password/load-secrets-action@v2 | |
| with: | |
| export-env: true | |
| env: | |
| OP_SERVICE_ACCOUNT_TOKEN: ${{ secrets.TRAINING_OP_SERVICE_ACCOUNT_TOKEN }} | |
| AWS_ACCESS_KEY_ID: ${{ secrets.OP_TRAINING_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.OP_TRAINING_SECRET_ACCESS_KEY }} | |
| - name: Download data from S3 | |
| env: | |
| AWS_DEFAULT_REGION: us-east-1 | |
| run: | | |
| aws s3 sync s3://ccdl-training-data/training-modules/ . | |
| - name: Render notebooks | |
| run: bash scripts/render-live.sh |