Merge pull request #62 from apeltzer/rootstock-2020-11-11

[ci skip] This build is based on 9444db7. This commit was created by the following CI build and job: https://github.com/apeltzer/eager2-paper/commit/9444db7443a66f375c7f2adbffbebb6541b512ea/checks https://github.com/apeltzer/eager2-paper/runs/358538661
apeltzer · Nov 11, 2020 · 41939e8 · 41939e8
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diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # Output directory containing the formatted manuscript
 
 The [`gh-pages`](https://github.com/apeltzer/eager2-paper/tree/gh-pages) branch hosts the contents of this directory at <https://apeltzer.github.io/eager2-paper/>.
-The permalink for this webpage version is <https://apeltzer.github.io/eager2-paper/v/385917553473f25918b140f8554374d9387c4eb1/>.
+The permalink for this webpage version is <https://apeltzer.github.io/eager2-paper/v/9444db7443a66f375c7f2adbffbebb6541b512ea/>.
 To redirect to the permalink for the latest manuscript version at anytime, use the link <https://apeltzer.github.io/eager2-paper/v/freeze/>.
 
 ## Files
@@ -35,4 +35,4 @@ Verifying timestamps with the `ots verify` command requires running a local bitc
 ## Source
 
 The manuscripts in this directory were built from
-[`385917553473f25918b140f8554374d9387c4eb1`](https://github.com/apeltzer/eager2-paper/commit/385917553473f25918b140f8554374d9387c4eb1).
+[`9444db7443a66f375c7f2adbffbebb6541b512ea`](https://github.com/apeltzer/eager2-paper/commit/9444db7443a66f375c7f2adbffbebb6541b512ea).
diff --git a/index.html b/index.html
@@ -13,7 +13,7 @@
   <meta name="author" content="Maxime U. Garcia" />
   <meta name="author" content="Judith Neukamm" />
   <meta name="author" content="Alexander Peltzer" />
-  <meta name="dcterms.date" content="2020-10-21" />
+  <meta name="dcterms.date" content="2020-11-11" />
   <meta name="keywords" content="nf-core, nextflow, ancientDNA, aDNA, palaeogenetics, archaeogenetics, bioinformatics" />
   <title>Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager</title>
   <style>
@@ -98,8 +98,8 @@
   <meta name="citation_title" content="Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager" />
   <meta property="og:title" content="Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager" />
   <meta property="twitter:title" content="Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager" />
-  <meta name="dc.date" content="2020-10-21" />
-  <meta name="citation_publication_date" content="2020-10-21" />
+  <meta name="dc.date" content="2020-11-11" />
+  <meta name="citation_publication_date" content="2020-11-11" />
   <meta name="dc.language" content="en-GB" />
   <meta name="citation_language" content="en-GB" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -149,13 +149,13 @@
   <meta name="citation_fulltext_html_url" content="https://apeltzer.github.io/eager2-paper/" />
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-  <link rel="alternate" type="text/html" href="https://apeltzer.github.io/eager2-paper/v/385917553473f25918b140f8554374d9387c4eb1/" />
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+  <link rel="alternate" type="text/html" href="https://apeltzer.github.io/eager2-paper/v/9444db7443a66f375c7f2adbffbebb6541b512ea/" />
+  <meta name="manubot_html_url_versioned" content="https://apeltzer.github.io/eager2-paper/v/9444db7443a66f375c7f2adbffbebb6541b512ea/" />
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   <meta property="og:type" content="article" />
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+  <meta property="og:image" content="https://github.com/apeltzer/eager2-paper/raw/9444db7443a66f375c7f2adbffbebb6541b512ea/content/images/nf-core-eager_social_preview.png" />
+  <meta property="twitter:image" content="https://github.com/apeltzer/eager2-paper/raw/9444db7443a66f375c7f2adbffbebb6541b512ea/content/images/nf-core-eager_social_preview.png" />
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@@ -167,10 +167,10 @@ <h1 class="title">Reproducible, portable, and efficient ancient genome reconstru
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://apeltzer.github.io/eager2-paper/v/385917553473f25918b140f8554374d9387c4eb1/">permalink</a>)
+(<a href="https://apeltzer.github.io/eager2-paper/v/9444db7443a66f375c7f2adbffbebb6541b512ea/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/apeltzer/eager2-paper/tree/385917553473f25918b140f8554374d9387c4eb1">apeltzer/eager2-paper@3859175</a>
-on October 21, 2020.
+from <a href="https://github.com/apeltzer/eager2-paper/tree/9444db7443a66f375c7f2adbffbebb6541b512ea">apeltzer/eager2-paper@9444db7</a>
+on November 11, 2020.
 </em></small></p>
 <h2 id="authors">Authors</h2>
 <ul>
@@ -647,7 +647,7 @@ <h2 id="comparisons-with-other-pipelines">Comparisons with other pipelines</h2>
 nf-core/eager is equivalent or more efficient than EAGER or PALEOMIX.</p>
 <div id="tbl:pipeline-comparison" class="tablenos">
 <table>
-<caption><span>Table 1:</span> Comparison of pipeline functionality of common ancient DNA processing
+<caption><span>Table 1:</span> Comparison of pipeline functionality of common ancient DNA processing
 pipelines. Tick represents full functionality, tilde represents partial functionality, and cross represents not implemented. </caption>
 <thead>
 <tr class="header">
@@ -890,7 +890,7 @@ <h2 id="comparisons-with-other-pipelines">Comparisons with other pipelines</h2>
 the GNU time tool (v1.7).</p>
 <div id="tbl:benchmarking-runtimes" class="tablenos">
 <table style="width:100%;">
-<caption><span>Table 2:</span> Comparison of run times in minutes between three ancient DNA pipelines.
+<caption><span>Table 2:</span> Comparison of run times in minutes between three ancient DNA pipelines.
 PALEOMIX and nf-core/eager have additional runs with ‘optimised’ parameters with
 fairer computational resources matching modern multi-threading strategies.
 Values represent mean and standard deviation of run times in minutes, calculated
@@ -1232,7 +1232,7 @@ <h3 id="pipeline-comparison">Pipeline Comparison</h3>
 variation across replicates as can be seen in Table <a href="#tbl:benchmarking-results">3</a>.</p>
 <div id="tbl:benchmarking-results" class="tablenos">
 <table>
-<caption><span>Table 3:</span> Comparison of common results values of key high-throughput short-read
+<caption><span>Table 3:</span> Comparison of common results values of key high-throughput short-read
 data processing and mapping steps across the three pipelines. ‘qf’ stands for
 mapping-quality filtered reads. All values represent mean and standard deviation
 across 10 replicates of each pipeline, calculated from the output of the GNU
@@ -1853,18 +1853,18 @@ <h2 class="page_break_before" id="references">References</h2>
 <div id="ref-ZEaeXPY6">
 <p>83. <strong>ATLAS: Analysis Tools for Low-depth and Ancient Samples</strong> <br />
 Vivian Link, Athanasios Kousathanas, Krishna Veeramah, Christian Sell, Amelie Scheu, Daniel Wegmann<br />
-<em>bioRxiv</em> (2017-03-24) <a href="https://doi.org/gg668z">https://doi.org/gg668z</a> <br />
+<em>Cold Spring Harbor Laboratory</em> (2017-03-24) <a href="https://doi.org/gg668z">https://doi.org/gg668z</a> <br />
 DOI: <a href="https://doi.org/10.1101/105346">10.1101/105346</a></p>
 </div>
 <div id="ref-NXbAmDI0">
 <p>84. <strong>nf-core/eager</strong> <br />
 nf-core<br />
-(2020-10-21) <a href="https://github.com/nf-core/eager">https://github.com/nf-core/eager</a></p>
+(2020-11-11) <a href="https://github.com/nf-core/eager">https://github.com/nf-core/eager</a></p>
 </div>
 <div id="ref-13kS0x2y1">
 <p>85. <strong>nf-core/configs</strong> <br />
 nf-core<br />
-(2020-09-29) <a href="https://github.com/nf-core/configs">https://github.com/nf-core/configs</a></p>
+(2020-11-10) <a href="https://github.com/nf-core/configs">https://github.com/nf-core/configs</a></p>
 </div>
 <div id="ref-1Bdq6PHHx">
 <p>86. <strong>MultiQC</strong> <a href="https://multiqc.info/">https://multiqc.info/</a></p>
@@ -2094,15 +2094,17 @@ <h2 class="page_break_before" id="references">References</h2>
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@@ -2682,7 +2684,8 @@ <h2 class="page_break_before" id="references">References</h2>
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@@ -2933,7 +2936,7 @@ <h2 class="page_break_before" id="references">References</h2>
 
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diff --git a/manuscript.pdf b/manuscript.pdf
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