update badge status and fixing naming

Author: lpantano

.github/workflows/run_visium_clustering.yaml

@@ -3,8 +3,12 @@ name: Visium Clustering and Annotation
 on:
   push:
     branches: [main]
+    paths:
+      - 'visium/02_clustering_annotation/02_clustering_annotation.qmd'
   pull_request:
     branches: [main]
+    paths:
+      - 'visium/02_clustering_annotation/02_clustering_annotation.qmd'
 
 jobs:
   r-visium-clustering:
@@ -53,13 +57,7 @@ jobs:
 
       - name: Run clustering and annotation
         id: render_qmd
-        run: |
-          if git diff --quiet origin/main -- visium/02_clustering_annotation/02_clustering_annotation.qmd; then
-            echo "No changes in 02_clustering_annotation.qmd. Skipping render."
-            exit 0
-          else
-            quarto render visium/02_clustering_annotation/02_clustering_annotation.qmd
-          fi
+        run: quarto render visium/02_clustering_annotation/clustering_annotation.qmd
         shell: bash
 
       - name: Deploy HTML to gh-pages
@@ -71,7 +69,7 @@ jobs:
           git switch gh-pages || git checkout -b gh-pages
           # mkdir -p visium/02_clustering_annotation
           # cp visium/02_clustering_annotation/02_clustering_annotation.html visium/02_clustering_annotation/
-          git add visium/02_clustering_annotation/02_clustering_annotation.html
-          git commit -m "Deploy 02_clustering_annotation.html [skip ci]" || echo "No changes to commit"
+          git add visium/02_clustering_annotation/clustering_annotation.html
+          git commit -m "Deploy clustering_annotation.html [skip ci]" || echo "No changes to commit"
           git push origin gh-pages
         shell: bash

.github/workflows/run_visium_qc.yaml

@@ -3,8 +3,12 @@ name: Visium Quality Control
 on:
   push:
     branches: [main]
+    paths:
+      - 'visium/01_quality_assessment/quality_assessment.qmd'
   pull_request:
     branches: [main]
+    paths:
+      - 'visium/01_quality_assessment/quality_assessment.qmd'
 
 jobs:
   r-visum-qc:
@@ -67,7 +71,7 @@ jobs:
           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
-          mkdir -p visium/01_quality_assessment
+          # mkdir -p visium/01_quality_assessment
           # cp visium/01_quality_assessment/quality_assessment.html visium/01_quality_assessment/
           git add visium/01_quality_assessment/quality_assessment.html
           git commit -m "Deploy quality_assessment.html [skip ci]" || echo "No changes to commit"

visium/01_quality_assessment/qc.Rmd

@@ -25,7 +25,7 @@ editor_options:
   chunk_output_type: console
 ---
 
-This code is in this ![](https://img.shields.io/badge/status-draft-grey) revision.
+This code is in this ![](https://img.shields.io/badge/status-alpha-yellow) revision.
 
 ## Visium Description
 

visium/01_quality_assessment/quality_assessment.qmd

@@ -24,7 +24,7 @@ params:
   scrna_refF: "../allen_ref_subset.qs"
 ---
 
-This code is in this ![](https://img.shields.io/badge/status-draft-grey) revision.
+This code is in this ![](https://img.shields.io/badge/status-alpha-yellow) revision.
 
 ```{r versioncheck, cache = FALSE, message = FALSE, warning=FALSE}
 # library(rstudioapi)