better readme #26
Workflow file for this run
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| name: Render R Markdown | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| render-rmd: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Install pandoc | |
| uses: pandoc/actions/setup@v1 | |
| - name: Run pandoc | |
| run: pandoc --version | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| # Cache R package installations | |
| - name: Cache R packages | |
| uses: actions/cache@v3 | |
| with: | |
| path: /home/runner/work/_temp/Library | |
| key: ${{ runner.os }}-R-${{ hashFiles('**/*.Rmd', '**/*.R') }} | |
| restore-keys: | | |
| ${{ runner.os }}-R- | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libcurl4-openssl-dev libfontconfig1-dev libfreetype6-dev libglpk40 | |
| # Check if QC.Rmd has changed | |
| - name: Check for changes in QC.Rmd | |
| id: check_changes | |
| run: | | |
| git diff --name-only ${{ github.event.before }} ${{ github.sha }} | grep -q "QC.Rmd" && echo "changed=true" || echo "changed=false" | |
| - name: Install necessary R packages | |
| if: steps.check_changes.outputs.changed == 'true' | |
| run: | | |
| R -e 'install.packages("BiocManager")' | |
| R -e 'BiocManager::install("renv")' | |
| R -e 'BiocManager::install(c("Rhtslib", "Rsamtools", "GenomicAlignments", "rtracklayer", "systemfonts"))' | |
| R -e 'BiocManager::install(renv::dependencies(path = "./01_quality_assessment/.")[["Package"]])' | |
| R -e 'BiocManager::install(renv::dependencies(path = "./00_libs/load_data.R")[["Package"]])' | |
| # Add any other package installations you need here | |
| # e.g., Rscript ./install_depedencies.R | |
| - name: Render R Markdown | |
| if: steps.check_changes.outputs.changed == 'true' | |
| run: | | |
| Rscript -e 'rmarkdown::render("QC.Rmd", quiet = TRUE)' | |
| working-directory: ./01_quality_assessment | |
| - name: Upload HTML report | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: rendered-report | |
| path: ./01_quality_assessment/QC.html |