add Heatmaps for logCPM, and Deseq2 pipelines #39
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| on: | |
| workflow_dispatch: | |
| push: | |
| branches: [main, master] | |
| name: Quarto Publish | |
| jobs: | |
| build-deploy: | |
| if: contains(github.event.head_commit.message, 'web generation') | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: write | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Install ImageMagick (for webp conversion and Heatmap rasterisation) | |
| uses: mfinelli/setup-imagemagick@v6.0.0 | |
| - name: Install system dependencies required for CRAN packages | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libcurl4-openssl-dev libglpk40 libmagick++-dev | |
| - name: Set up Quarto | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| tinytex: true # required for pdf outputs | |
| - name: Install R version | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: '4.2.1' | |
| - name: Install LOCAL Renv R Dependencies | |
| uses: r-lib/actions/setup-renv@v2 | |
| - name: Render and Publish | |
| uses: quarto-dev/quarto-actions/publish@v2 | |
| with: | |
| target: gh-pages | |
| # render: false | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |