bulk-rnaseq-differential-expression/.github/workflows/ci.yml at ec025422504b0bb3bfdcd36adf4825f80501c36c · Ekin-Kahraman/bulk-rnaseq-differential-expression · GitHub

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name: CI

on:
  push:
  pull_request:

jobs:
  r-checks:
    runs-on: ubuntu-latest

    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Install system dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y \
            libcairo2-dev \
            libcurl4-openssl-dev \
            libfontconfig1-dev \
            libglpk-dev \
            libpng-dev \
            libx11-dev \
            pandoc

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: "4.5.2"
          use-public-rspm: false

      - name: Restore renv packages
        uses: r-lib/actions/setup-renv@v2

      - name: Restore pinned dependencies
        run: Rscript 000_install_dependencies.R

      - name: Verify renv.lock unchanged
        run: git diff --exit-code renv.lock

      - name: Check renv status
        run: >
          Rscript -e 's <- renv::status();
          if (is.list(s) && !isTRUE(s$synchronized)) quit(status = 1)'

      - name: Lint
        run: Rscript dev/lint.R

      - name: Tests
        run: Rscript -e 'testthat::test_dir("tests/testthat")'

  pipeline-rebuild:
    runs-on: ubuntu-latest

    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Install system dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y \
            libcairo2-dev \
            libcurl4-openssl-dev \
            libfontconfig1-dev \
            libglpk-dev \
            libpng-dev \
            libx11-dev \
            pandoc

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: "4.5.2"
          use-public-rspm: false

      - name: Restore renv packages
        uses: r-lib/actions/setup-renv@v2

      - name: Install pinned dependencies
        run: Rscript 000_install_dependencies.R

      - name: Save tracked tables for comparison
        run: |
          mkdir -p "$RUNNER_TEMP/reference_tables"
          cp results/tables/*.csv "$RUNNER_TEMP/reference_tables"/

      - name: Remove committed analysis outputs before rebuild
        run: rm -f results/figures/*.png results/tables/*.csv

      - name: Rebuild analysis outputs
        run: Rscript run_all.R

      - name: Validate rebuilt outputs
        run: Rscript -e 'testthat::test_dir("tests/testthat")'

      - name: Compare regenerated tables to tracked results
        run: Rscript dev/compare_tables.R "$RUNNER_TEMP/reference_tables" results/tables

      - name: Verify key figures were regenerated
        run: |
          test -f results/figures/qc_library_size.png
          test -f results/figures/ma_plot.png
          test -f results/figures/pca_plot.png
          test -f results/figures/sensitivity_lfc_scatter.png
          test -f results/figures/volcano_plot.png