improve pushing to gh-pages

Author: lpantano

.github/workflows/run_scrna_qc.yml

@@ -66,9 +66,27 @@ jobs:
         run: |
           git config --global user.name "github-actions[bot]"
           git config --global user.email "github-actions[bot]@users.noreply.github.com"
-          git fetch origin gh-pages || git checkout --orphan gh-pages
-          git switch gh-pages || git checkout -b gh-pages
+          # Fetch gh-pages branch (create if missing)
+          OUTPUT_FILE="01_quality_assessment/scRNA_QC.html"
+
+          git fetch origin gh-pages || true
+          if git show-ref --verify --quiet refs/remotes/origin/gh-pages; then
+            git checkout gh-pages
+            git merge --strategy=ours origin/gh-pages
+          else
+            git checkout --orphan gh-pages
+          fi
+
+          # Copy the HTML file into place (keep existing files)
+          mkdir -p 01_quality_assessment
+          cp "$OUTPUT_FILE" 01_quality_assessment/
+
+          # Commit only if changes exist
           git add 01_quality_assessment/scRNA_QC.html
-          git commit -m "Deploy scRNA_QC.html [skip ci]" || echo "No changes to commit"
-          git push origin gh-pages
+          if git diff --cached --quiet; then
+            echo "No changes to commit"
+          else
+            git commit -m "Deploy scRNA_QC.html [skip ci]"
+            git push origin gh-pages
+          fi
         shell: bash