fix push to gh-pages

Author: lpantano

.github/workflows/03_run_scrna_mast.yml

@@ -91,11 +91,9 @@ jobs:
           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 "$(dirname "$OUTPUT_FILE")/$(basename "$OUTPUT_FILE")"
-            git commit -m "Deploy $(basename "$OUTPUT_FILE") [skip ci]"
-            git push origin gh-pages
-          fi
+          
+          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/03_run_scrna_pseudobulk.yml

@@ -80,11 +80,7 @@ jobs:
           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 "$(dirname "$OUTPUT_FILE")/$(basename "$OUTPUT_FILE")"
-            git commit -m "Deploy $(basename "$OUTPUT_FILE") [skip ci]"
-            git push origin gh-pages
-          fi
+          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

README.md

@@ -39,11 +39,13 @@ This template has guidelines on how to work with multiple samples. It compares l
 
 # Differential Expression
 
-Read full documentation at [02_differential_expression/README.md](02_differential_expression/README.md).
+Read full documentation at [03_differential_expression/README.md](03_differential_expression/README.md).
 
--   pseudobulk approach: ![](https://img.shields.io/badge/status-alpha-yellow) [`02_differential_expression/scRNA_pseudobulk.Rmd`](02_differential_expression/scRNA_pseudobulk.Rmd) is a template that performs pseudobulk differential expression analysis using DESeq2.
+-   ![](https://img.shields.io/badge/status-stable-green) [scRNA_pseudobulk](03_differential_expression/scRNA_pseudobulk.qmd) is a template that performs pseudobulk differential expression analysis using DESeq2. 👀 [See an example](https://bcbio.github.io/singlecell-reports/03_differential_expression/scRNA_pseudobulk.html)
 
--   MAST - single cell approach: ![](https://img.shields.io/badge/status-alpha-yellow) [`02_differential_expression/scRNA_MAST.Rmd`](02_differential_expression/scRNA_MAST.Rmd) is a template to visualize differentially expressed genes (DEG) results generated from MAST analysis. \## Compositional Analysis
+- ![](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