update actions

.github/workflows/00_run_readme.yml

@@ -0,0 +1,52 @@
+name: Quality Control
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - 'README.md'
+  pull_request:
+    branches: [main]
+    paths:
+      - 'README.md'
+  workflow_dispatch:
+
+jobs:
+  readme:
+    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: Deploy RMD 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="README.md"
+
+          # Create a temporary worktree for gh-pages branch
+          git fetch origin gh-pages || true
+          git worktree add /tmp/gh-pages gh-pages || git worktree add /tmp/gh-pages -b gh-pages
+
+          # Copy the file to the worktree
+          cp "$OUTPUT_FILE" /tmp/gh-pages/
+
+          cd /tmp/gh-pages
+
+          # Commit and push if there are changes
+          git add README.md
+          git commit -m "Deploy README.md [skip ci]"
+          git push --force origin gh-pages
+
+          # Clean up
+          cd -
+          git worktree remove /tmp/gh-pages
+        shell: bash

.github/workflows/01_run_scrna_qc.yml

@@ -68,26 +68,18 @@ jobs:
           git config --global user.email "github-actions[bot]@users.noreply.github.com"
           OUTPUT_FILE="01_quality_assessment/scRNA_QC.html"
 
-          # Create a temporary worktree for gh-pages branch
+          # Fetch gh-pages (if exists) and create worktree
           git fetch origin gh-pages || true
-          git worktree add /tmp/gh-pages gh-pages || git worktree add /tmp/gh-pages -b gh-pages
+          git worktree add /tmp/gh-pages gh-pages 2>/dev/null || git worktree add /tmp/gh-pages -b gh-pages
 
-          # Copy the file to the worktree
-          mkdir -p /tmp/gh-pages/01_quality_assessment
-          cp "$OUTPUT_FILE" /tmp/gh-pages/01_quality_assessment/
+          # Copy the file into the worktree
+          mkdir -p "/tmp/gh-pages/$(dirname "$OUTPUT_FILE")"
+          cp "$OUTPUT_FILE" "/tmp/gh-pages/$(dirname "$OUTPUT_FILE")/"
 
           cd /tmp/gh-pages
 
           # Commit and push if there are changes
-          if git diff --quiet && git diff --cached --quiet; then
-            echo "No changes to commit"
-          else
-            git add 01_quality_assessment/scRNA_QC.html
-            git commit -m "Deploy scRNA_QC.html [skip ci]"
-            git push origin gh-pages
-          fi
-
-          # Clean up
-          cd -
-          git worktree remove /tmp/gh-pages
+          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

.github/workflows/02_run_norm_integration.yml

@@ -69,22 +69,18 @@ jobs:
 
           OUTPUT_FILE="02_integration/norm_integration.html"
 
-          # Create a temporary worktree for gh-pages branch
+          # Fetch gh-pages (if exists) and create worktree
           git fetch origin gh-pages || true
-          git worktree add /tmp/gh-pages gh-pages || git worktree add /tmp/gh-pages -b gh-pages
+          git worktree add /tmp/gh-pages gh-pages 2>/dev/null || git worktree add /tmp/gh-pages -b gh-pages
 
-          # Copy the file to the worktree
-          mkdir -p /tmp/gh-pages/02_integration
-          cp "$OUTPUT_FILE" /tmp/gh-pages/02_integration/
+          # Copy the file into the worktree
+          mkdir -p "/tmp/gh-pages/$(dirname "$OUTPUT_FILE")"
+          cp "$OUTPUT_FILE" "/tmp/gh-pages/$(dirname "$OUTPUT_FILE")/"
 
           cd /tmp/gh-pages
-          ls -R .
 
-          git add 02_integration/norm_integration.html
-          git commit -m "Deploy norm_integration.html [skip ci]"
+          # 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
-
-          # Clean up
-          cd -
-          git worktree remove /tmp/gh-pages
         shell: bash

README.md

@@ -45,8 +45,6 @@ Read full documentation at [03_differential_expression/README.md](03_differentia
 
 - ![](https://img.shields.io/badge/status-stable-green) [MAST scRNA](03_differential_expression/scRNA_MAST.Rmd) is a template to visualize differentially expressed genes (DEG) results generated from MAST analysis. 👀 [See an example](https://bcbio.github.io/singlecell-reports/03_differential_expression/scRNA_MAST.html)
 
-## Compositional Analysis
-
 # Compositional Analysis
 
 ![](https://img.shields.io/badge/status-draft-grey) [`04_compositional/propeller.Rmd`](04_compositional/propeller.Rmd) and [`04_compositional/sscomp.Rmd`](04_compositional/sccomp.Rmd) are templates to run compositional analysis with two different methods. `comp.png` is an example of `sccomp.Rmd` analysis.