Deploy preview for PR 96 🛫

openpipelines-bio · Aug 22, 2024 · 092367a · 092367a
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diff --git a/pr-preview/pr-96/CHANGELOG.html b/pr-preview/pr-96/CHANGELOG.html
@@ -107,7 +107,7 @@
   </li>  
   <li class="nav-item">
     <a class="nav-link" href="./user_guide/index.html"> 
-<span class="menu-text">User Guide</span></a>
+<span class="menu-text">User guide</span></a>
   </li>  
   <li class="nav-item">
     <a class="nav-link" href="./contributing/index.html"> 

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diff --git a/pr-preview/pr-96/components/modules/velocity/velocyto.html b/pr-preview/pr-96/components/modules/velocity/velocyto.html
diff --git a/pr-preview/pr-96/components/workflows/gdo/gdo_singlesample.html b/pr-preview/pr-96/components/workflows/gdo/gdo_singlesample.html
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diff --git a/pr-preview/pr-96/components/workflows/multiomics/dimensionality_reduction.html b/pr-preview/pr-96/components/workflows/multiomics/dimensionality_reduction.html
diff --git a/pr-preview/pr-96/components/workflows/multiomics/process_batches.html b/pr-preview/pr-96/components/workflows/multiomics/process_batches.html
diff --git a/pr-preview/pr-96/components/workflows/multiomics/process_samples.html b/pr-preview/pr-96/components/workflows/multiomics/process_samples.html
diff --git a/pr-preview/pr-96/components/workflows/multiomics/split_modalities.html b/pr-preview/pr-96/components/workflows/multiomics/split_modalities.html
diff --git a/pr-preview/pr-96/components/workflows/prot/prot_multisample.html b/pr-preview/pr-96/components/workflows/prot/prot_multisample.html
diff --git a/pr-preview/pr-96/components/workflows/prot/prot_singlesample.html b/pr-preview/pr-96/components/workflows/prot/prot_singlesample.html
diff --git a/pr-preview/pr-96/components/workflows/qc/qc.html b/pr-preview/pr-96/components/workflows/qc/qc.html
diff --git a/pr-preview/pr-96/components/workflows/rna/rna_multisample.html b/pr-preview/pr-96/components/workflows/rna/rna_multisample.html
diff --git a/pr-preview/pr-96/components/workflows/rna/rna_singlesample.html b/pr-preview/pr-96/components/workflows/rna/rna_singlesample.html
diff --git a/pr-preview/pr-96/contributing/creating_components.html b/pr-preview/pr-96/contributing/creating_components.html
@@ -137,15 +137,15 @@
 <span class="menu-text">Home</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../fundamentals/index.html"> 
+    <a class="nav-link active" href="../fundamentals/index.html" aria-current="page"> 
 <span class="menu-text">Fundamentals</span></a>
   </li>  
   <li class="nav-item">
     <a class="nav-link" href="../user_guide/index.html"> 
-<span class="menu-text">User Guide</span></a>
+<span class="menu-text">User guide</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link active" href="../contributing/index.html" aria-current="page"> 
+    <a class="nav-link" href="../contributing/index.html"> 
 <span class="menu-text">Contributing</span></a>
   </li>  
   <li class="nav-item">
@@ -188,15 +188,103 @@
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a href="../contributing/index.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Contributing</span></a>
+            <a href="../fundamentals/index.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Fundamentals</span></a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" role="navigation" aria-expanded="true" aria-label="Toggle section">
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       </div>
       <ul id="quarto-sidebar-section-1" class="collapse list-unstyled sidebar-section depth1 show">  
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+  <a href="../fundamentals/philosophy.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Philosophy</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../fundamentals/concepts.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Concepts</span></a>
+  </div>
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+  <a href="../fundamentals/architecture.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Architecture</span></a>
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+  <div class="sidebar-item-container"> 
+  <a href="../fundamentals/roadmap.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Roadmap</span></a>
+  </div>
+</li>
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+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a href="../user_guide/index.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">User guide</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" role="navigation" aria-expanded="true" aria-label="Toggle section">
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+      <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../user_guide/getting_started.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Getting started</span></a>
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+  <div class="sidebar-item-container"> 
+  <a href="../user_guide/running_pipelines.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Running pipelines</span></a>
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+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../user_guide/parameter_lists.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Passing parameter lists</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../user_guide/ingestion.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Ingestion</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../user_guide/processing.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Processing</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../user_guide/downstream.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Downstream</span></a>
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+  <div class="sidebar-item-container"> 
+  <a href="../user_guide/bug_reports.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Bug reports</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a href="../contributing/index.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Contributing</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" role="navigation" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../contributing/getting_started.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Getting started</span></a>
   </div>
@@ -230,6 +318,35 @@
   <a href="../contributing/pull_requests.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Publishing your changes</span></a>
   </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a href="../more_information/index.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">More information</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" role="navigation" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-4" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../more_information/cheat_sheets.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Cheat sheets</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../more_information/code_of_conduct.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Code of conduct</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../more_information/faq.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">FAQ</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/pr-preview/pr-96/contributing/creating_pipelines.html b/pr-preview/pr-96/contributing/creating_pipelines.html
@@ -103,15 +103,15 @@
 <span class="menu-text">Home</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="../fundamentals/index.html"> 
+    <a class="nav-link active" href="../fundamentals/index.html" aria-current="page"> 
 <span class="menu-text">Fundamentals</span></a>
   </li>  
   <li class="nav-item">
     <a class="nav-link" href="../user_guide/index.html"> 
-<span class="menu-text">User Guide</span></a>
+<span class="menu-text">User guide</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link active" href="../contributing/index.html" aria-current="page"> 
+    <a class="nav-link" href="../contributing/index.html"> 
 <span class="menu-text">Contributing</span></a>
   </li>  
   <li class="nav-item">
@@ -154,15 +154,103 @@
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
-            <a href="../contributing/index.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Contributing</span></a>
+            <a href="../fundamentals/index.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Fundamentals</span></a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" role="navigation" aria-expanded="true" aria-label="Toggle section">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
       </div>
       <ul id="quarto-sidebar-section-1" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
+  <a href="../fundamentals/philosophy.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Philosophy</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../fundamentals/concepts.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Concepts</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../fundamentals/architecture.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Architecture</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../fundamentals/roadmap.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Roadmap</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a href="../user_guide/index.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">User guide</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" role="navigation" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../user_guide/getting_started.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Getting started</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../user_guide/running_pipelines.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Running pipelines</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../user_guide/parameter_lists.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Passing parameter lists</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../user_guide/ingestion.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Ingestion</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../user_guide/processing.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Processing</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../user_guide/downstream.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Downstream</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../user_guide/bug_reports.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Bug reports</span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a href="../contributing/index.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Contributing</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" role="navigation" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
   <a href="../contributing/getting_started.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Getting started</span></a>
   </div>
@@ -196,6 +284,35 @@
   <a href="../contributing/pull_requests.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Publishing your changes</span></a>
   </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a href="../more_information/index.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">More information</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" role="navigation" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-4" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../more_information/cheat_sheets.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Cheat sheets</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../more_information/code_of_conduct.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Code of conduct</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../more_information/faq.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">FAQ</span></a>
+  </div>
 </li>
       </ul>
   </li>