Merge pull request #15 from AlexsLemonade/cgreene-methods-headers

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8993eb4.

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Merge pull request #15 from AlexsLemonade/cgreene-methods-headers

add headers for data processing sections

manuscript.html

@@ -6,7 +6,7 @@
   <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
   <meta name="author" content="John Doe" />
   <meta name="author" content="Jane Roe" />
-  <meta name="dcterms.date" content="2019-07-14" />
+  <meta name="dcterms.date" content="2019-07-15" />
   <meta name="keywords" content="pediatric cancer, brain tumor, tumor atlas" />
   <title>An Open Pediatric Brain Tumor Atlas</title>
   <style>
@@ -23,7 +23,7 @@
 <header id="title-block-header">
 <h1 class="title">An Open Pediatric Brain Tumor Atlas</h1>
 </header>
-<p><small><em> This manuscript (<a href="https://AlexsLemonade.github.io/OpenPBTA-manuscript/v/34b8e1ab138c1e04315996d53acd7fef40060b5d/">permalink</a>) was automatically generated from <a href="https://github.com/AlexsLemonade/OpenPBTA-manuscript/tree/34b8e1ab138c1e04315996d53acd7fef40060b5d">AlexsLemonade/OpenPBTA-manuscript@34b8e1a</a> on July 14, 2019. </em></small></p>
+<p><small><em> This manuscript (<a href="https://AlexsLemonade.github.io/OpenPBTA-manuscript/v/8993eb4e2751aee9f671a9ed4fb5a2de2ca062b5/">permalink</a>) was automatically generated from <a href="https://github.com/AlexsLemonade/OpenPBTA-manuscript/tree/8993eb4e2751aee9f671a9ed4fb5a2de2ca062b5">AlexsLemonade/OpenPBTA-manuscript@8993eb4</a> on July 15, 2019. </em></small></p>
 <h2 id="authors">Authors</h2>
 <ul>
 <li><p><strong>John Doe</strong><br> <img src="images/orcid.svg" alt="ORCID icon" class="inline_icon" /> <a href="https://orcid.org/XXXX-XXXX-XXXX-XXXX">XXXX-XXXX-XXXX-XXXX</a> · <img src="images/github.svg" alt="GitHub icon" class="inline_icon" /> <a href="https://github.com/johndoe">johndoe</a> · <img src="images/twitter.svg" alt="Twitter icon" class="inline_icon" /> <a href="https://twitter.com/johndoe">johndoe</a><br> <small> Department of Something, University of Whatever · Funded by Grant XXXXXXXX </small></p></li>
@@ -32,6 +32,18 @@ <h2 id="authors">Authors</h2>
 <h2 id="abstract" class="page_break_before">Abstract</h2>
 <h2 id="introduction">Introduction</h2>
 <p>Introduction will go here.</p>
+<h2 id="materials-and-methods">Materials and Methods</h2>
+<h3 id="childrens-brain-tumor-tissue-consortium-data">Children’s Brain Tumor Tissue Consortium Data</h3>
+<h3 id="pediatric-pacific-neuro-oncology-consortium-data">Pediatric Pacific Neuro-oncology Consortium Data</h3>
+<h3 id="germ-line-single-nucleotide-variant-calling">Germ Line Single Nucleotide Variant Calling</h3>
+<h3 id="germ-line-copy-number-variant-calling">Germ Line Copy Number Variant Calling</h3>
+<h3 id="germ-line-structural-variant-calling">Germ Line Structural Variant Calling</h3>
+<h3 id="somatic-single-nucleotide-variant-calling">Somatic Single Nucleotide Variant Calling</h3>
+<h3 id="somatic-copy-number-variant-calling">Somatic Copy Number Variant Calling</h3>
+<h3 id="somatic-structural-variant-calling">Somatic Structural Variant Calling</h3>
+<h3 id="gene-expression-abundance-estimation">Gene Expression Abundance Estimation</h3>
+<h3 id="rna-fusion-calling-and-prioritization">RNA Fusion Calling and Prioritization</h3>
+<h3 id="clinical-data-harmonization">Clinical Data Harmonization</h3>
 <h2 id="results">Results</h2>
 <p>Results section stub.</p>
 <h2 id="conclusions">Conclusions</h2>

manuscript.md

@@ -2,7 +2,7 @@
 author-meta:
 - John Doe
 - Jane Roe
-date-meta: '2019-07-14'
+date-meta: '2019-07-15'
 keywords:
 - pediatric cancer
 - brain tumor
@@ -18,10 +18,10 @@ title: An Open Pediatric Brain Tumor Atlas
 
 <small><em>
 This manuscript
-([permalink](https://AlexsLemonade.github.io/OpenPBTA-manuscript/v/34b8e1ab138c1e04315996d53acd7fef40060b5d/))
+([permalink](https://AlexsLemonade.github.io/OpenPBTA-manuscript/v/8993eb4e2751aee9f671a9ed4fb5a2de2ca062b5/))
 was automatically generated
-from [AlexsLemonade/OpenPBTA-manuscript@34b8e1a](https://github.com/AlexsLemonade/OpenPBTA-manuscript/tree/34b8e1ab138c1e04315996d53acd7fef40060b5d)
-on July 14, 2019.
+from [AlexsLemonade/OpenPBTA-manuscript@8993eb4](https://github.com/AlexsLemonade/OpenPBTA-manuscript/tree/8993eb4e2751aee9f671a9ed4fb5a2de2ca062b5)
+on July 15, 2019.
 </em></small>
 
 ## Authors
@@ -61,6 +61,31 @@ on July 14, 2019.
 Introduction will go here.
 
 
+## Materials and Methods
+
+### Children's Brain Tumor Tissue Consortium Data
+
+### Pediatric Pacific Neuro-oncology Consortium Data
+
+### Germ Line Single Nucleotide Variant Calling
+
+### Germ Line Copy Number Variant Calling
+
+### Germ Line Structural Variant Calling
+
+### Somatic Single Nucleotide Variant Calling
+
+### Somatic Copy Number Variant Calling
+
+### Somatic Structural Variant Calling
+
+### Gene Expression Abundance Estimation
+
+### RNA Fusion Calling and Prioritization
+
+### Clinical Data Harmonization
+
+
 ## Results
 
 Results section stub.

variables.json

@@ -1,5 +1,5 @@
 {
-  "date": "July 14, 2019",
+  "date": "July 15, 2019",
   "authors": [
     {
       "github": "johndoe",
@@ -46,12 +46,12 @@
     "repo_slug": "AlexsLemonade/OpenPBTA-manuscript",
     "repo_owner": "AlexsLemonade",
     "repo_name": "OpenPBTA-manuscript",
-    "commit": "34b8e1ab138c1e04315996d53acd7fef40060b5d"
+    "commit": "8993eb4e2751aee9f671a9ed4fb5a2de2ca062b5"
   },
   "manuscript_stats": {
     "reference_counts": {
       "total": 0
     },
-    "word_count": 249
+    "word_count": 318
   }
 }