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

This build is based on
8993eb4.

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https://travis-ci.com/AlexsLemonade/OpenPBTA-manuscript/builds/119163562
https://travis-ci.com/AlexsLemonade/OpenPBTA-manuscript/jobs/216129598

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The full commit message that triggered this build is copied below:

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

add headers for data processing sections

README.md

@@ -1,7 +1,7 @@
 # Output directory containing the formatted manuscript
 
 The [`gh-pages`](https://github.com/AlexsLemonade/OpenPBTA-manuscript/tree/gh-pages) branch hosts the contents of this directory at https://AlexsLemonade.github.io/OpenPBTA-manuscript/.
-The permalink for this webpage version is https://AlexsLemonade.github.io/OpenPBTA-manuscript/v/34b8e1ab138c1e04315996d53acd7fef40060b5d/.
+The permalink for this webpage version is https://AlexsLemonade.github.io/OpenPBTA-manuscript/v/8993eb4e2751aee9f671a9ed4fb5a2de2ca062b5/.
 To redirect to the permalink for the latest manuscript version at anytime, use the link https://AlexsLemonade.github.io/OpenPBTA-manuscript/v/freeze/.
 
 ## Files
@@ -36,4 +36,4 @@ Verifying timestamps with the `ots verify` command requires running a local bitc
 ## Source
 
 The manuscripts in this directory were built from
-[`34b8e1ab138c1e04315996d53acd7fef40060b5d`](https://github.com/AlexsLemonade/OpenPBTA-manuscript/commit/34b8e1ab138c1e04315996d53acd7fef40060b5d).
+[`8993eb4e2751aee9f671a9ed4fb5a2de2ca062b5`](https://github.com/AlexsLemonade/OpenPBTA-manuscript/commit/8993eb4e2751aee9f671a9ed4fb5a2de2ca062b5).

index.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>