Merge branch 'master' into set_up_azure_batch_pool

.github/workflows/build-nightly.yml

@@ -0,0 +1,12 @@
+name: Trigger Netlify Build
+on:
+  schedule:
+    - cron: '0 2 * * *' # Once a day
+  workflow_dispatch: # On demand
+jobs:
+  build:
+    name: Request Netlify Webhook
+    runs-on: ubuntu-latest
+    steps:
+      - name: POST to Build Hook
+        run: curl -X POST -d {} ${{ secrets.NETLIFY_BUILD_HOOK_URL }}

internal/fetch-docs-oss.mjs

@@ -9,33 +9,38 @@ const __dirname = path.dirname(__filename);
 
 const repositories = [
   {
-    name: 'multiqc',
-    url: 'https://github.com/MultiQC/MultiQC.git',
-    path: path.join(__dirname, "..", "multiqc_docs", "multiqc_repo")
+    name: "multiqc",
+    url: "https://github.com/MultiQC/MultiQC.git",
+    path: path.join(__dirname, "..", "multiqc_docs", "multiqc_repo"),
+    branch: "main",
   },
   {
-    name: 'wave',
-    url: 'https://github.com/seqeralabs/wave.git',
-    path: path.join(__dirname, "..", "wave_docs", "wave_repo")
-  }
+    name: "wave",
+    url: "https://github.com/seqeralabs/wave.git",
+    path: path.join(__dirname, "..", "wave_docs", "wave_repo"),
+    branch: "master",
+  },
 ];
 
 // Function to clone or update a repository
-async function cloneOrUpdateRepo({ name, url, path: repoPath }) {
+async function cloneOrUpdateRepo({ name, url, path: repoPath, branch }) {
   const exists = await fs.pathExists(repoPath + "/.git");
-  
+
   try {
     if (exists) {
-      console.log(`${name}: Cloned repo already exists, will pull latest changes`);
-      await git(repoPath).pull();
+      console.log(
+        `${name}: Cloned repo already exists, will pull latest changes`,
+      );
+      // pull and checkout the branch
+      await git(repoPath).pull("origin", branch);
       console.log(`✅ ${name}: Pulled latest changes`);
     } else {
       console.log(`${name}: Cloning into ${repoPath}`);
       await git().clone(url, repoPath);
       console.log(`✅ ${name}: Cloned`);
     }
   } catch (error) {
-    console.error(`❌ Error processing ${repo.name}:`);
+    console.error(`❌ Error processing ${repoPath}:`);
     console.error(error.message);
     if (exists) {
       console.error(`Try removing the directory: ${repoPath}`);
@@ -59,4 +64,4 @@ async function processRepositories() {
 }
 
 // Execute
-processRepositories().catch(console.error);
+processRepositories().catch(console.error);