03_run_scrna_pseudobulk.yml

name: scRNA Pseudobulk Analysis

on:
  push:
    branches: [main]
    paths:
      - '03_differential_expression/scRNA_pseudobulk.qmd'
  pull_request:
    branches: [main]
    paths:
      - '03_differential_expression/scRNA_pseudobulk.qmd'
  workflow_dispatch:

jobs:
  r-pseudobulk:
    runs-on: ubuntu-22.04

    env:
      RENV_PATHS_ROOT: ~/.local/share/renv  # persistent cache location

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

      - name: Install pandoc
        run: sudo apt-get update && sudo apt-get install -y pandoc

      - name: Set up R
        uses: r-lib/actions/setup-r@v2

      - name: Install system dependencies for R packages
        run: |
          sudo apt-get update
          sudo apt-get install -y build-essential libcurl4-openssl-dev libssl-dev libxml2-dev libgit2-dev libmagick++-dev libharfbuzz-dev libfribidi-dev libglpk-dev
        shell: bash

      - name: Cache R packages (renv)
        uses: actions/cache@v4
        with:
          path: ${{ env.RENV_PATHS_ROOT }}
          key: ${{ runner.os }}-renv-${{ hashFiles('03_differential_expression/renv.lock') }}
          restore-keys: |
            ${{ runner.os }}-renv-

      - name: Set repositories
        run: Rscript ubuntu.R

      - name: Restore environment from renv.lock
        run: |
          install.packages("renv", repos = "https://cloud.r-project.org")
          renv::restore(prompt = FALSE, lockfile = "03_differential_expression/renv.lock")
        shell: Rscript {0}
     
      - name: Set up Quarto
        uses: quarto-dev/quarto-actions/setup@v2
     
      - name: Run pseudobulk analysis
        id: render_qmd
        run: |
          cd 03_differential_expression
          quarto render scRNA_pseudobulk.qmd
        shell: bash

      - name: Deploy HTML to gh-pages
        if: success()
        run: |
          git config --global user.name "github-actions[bot]"
          git config --global user.email "github-actions[bot]@users.noreply.github.com"

          OUTPUT_FILE="03_differential_expression/scRNA_pseudobulk.html"

          # Fetch gh-pages (if exists) and create worktree
          git fetch origin gh-pages || true
          git worktree add /tmp/gh-pages gh-pages 2>/dev/null || git worktree add /tmp/gh-pages -b gh-pages

          # Copy the file into the worktree
          mkdir -p "/tmp/gh-pages/$(dirname "$OUTPUT_FILE")"
          cp "$OUTPUT_FILE" "/tmp/gh-pages/$(dirname "$OUTPUT_FILE")/"

          cd /tmp/gh-pages

          # Commit and push if there are changes
          git add "$(dirname "$OUTPUT_FILE")/$(basename "$OUTPUT_FILE")"
          git commit -m "Deploy $(basename "$OUTPUT_FILE") [skip ci]"
          git push --force origin gh-pages
        shell: bash