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% For more detailed article preparation guidelines, please see: http://wellcomeopenresearch.org/for-authors/article-guidelines and http://wellcomeopenresearch.org/for-authors/data-guidelines
% Options for packages loaded elsewhere - from Pandoc's template
\PassOptionsToPackage{unicode$for(hyperrefoptions)$,$hyperrefoptions$$endfor$}{hyperref}
\PassOptionsToPackage{hyphens}{url}
$if(colorlinks)$
\PassOptionsToPackage{dvipsnames,svgnames,x11names}{xcolor}
$endif$
\documentclass[10pt,a4paper,twocolumn]{article}
\usepackage{WellcomeOR_styles}

% hyperref required
\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}

% Link coloring
% Link coloring
\hypersetup{
$if(title-meta)$
  pdftitle={$title-meta$},
$endif$
$if(author-meta)$
  pdfauthor={$author-meta$},
$endif$
$if(lang)$
  pdflang={$lang$},
$endif$
$if(subject)$
  pdfsubject={$subject$},
$endif$
$if(keywords)$
  pdfkeywords={$for(keywords)$$keywords$$sep$, $endfor$},
$endif$
$if(colorlinks)$
  colorlinks=true,
  linkcolor={$if(linkcolor)$$linkcolor$$else$Maroon$endif$},
  filecolor={$if(filecolor)$$filecolor$$else$Maroon$endif$},
  citecolor={$if(citecolor)$$citecolor$$else$Blue$endif$},
  urlcolor={$if(urlcolor)$$urlcolor$$else$Blue$endif$},
$else$
  hidelinks,
$endif$
  pdfcreator={LaTeX via pandoc}}


$if(natbib)$
\usepackage[$if(natbiboptions)$$natbiboptions$$else$numbers$endif$]{natbib}
$endif$

% Pandoc toggle for numbering sections
$if(numbersections)$
\setcounter{secnumdepth}{$if(secnumdepth)$$secnumdepth$$else$5$endif$}
$else$
\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
$endif$

% Pandoc syntax highlighting
$if(highlighting-macros)$
$highlighting-macros$
$endif$

% tightlist command for lists without linebreak
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}

$if(tables)$
% From pandoc table feature
\usepackage{longtable,booktabs,array}
$if(multirow)$
\usepackage{multirow}
$endif$
\usepackage{calc} % for calculating minipage widths
% Correct order of tables after \paragraph or \subparagraph
\usepackage{etoolbox}
\makeatletter
\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
\makeatother
% Allow footnotes in longtable head/foot
\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
\makesavenoteenv{longtable}
$endif$

% Pandoc citation processing
$if(csl-refs)$
\newlength{\csllabelwidth}
\setlength{\csllabelwidth}{3em}
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
% for Pandoc 2.8 to 2.10.1
\newenvironment{cslreferences}%
  {$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
\everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
  {\par}
% For Pandoc 2.11+
\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing
 {% don't indent paragraphs
\setlength{\parindent}{0pt}
% turn on hanging indent if param 1 is 1
\ifodd #1 \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces\fi
% set entry spacing
\ifnum #2 > 0
\setlength{\parskip}{#2\baselineskip}
\fi
 }%
 {}
\usepackage{calc} % for calculating minipage widths
\newcommand{\CSLBlock}[1]{#1\hfill\break}
\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}

$endif$

$for(header-includes)$
  $header-includes$
$endfor$

\begin{document}

\title{$title$}
$if(titlenote)$
  \titlenote{$titlenote$}
$endif$

$for(author)$
  \author[$for(author.affil)$$author.affil$$sep$,$endfor$$if(author.corresponding)$*$endif$]{$author.name$}
$endfor$

$for(address)$
  \affil[$address.code$]{$address.address$}
$endfor$


\maketitle
\thispagestyle{fancy}

$for(author)$
    $author.name$: $author.email$\\
$endfor$
* Corresponding author\\

$for(include-before)$
  $include-before$

$endfor$

\begin{abstract}
$abstract$
\end{abstract}

\section*{Keywords}
$keywords$

\clearpage

$body$


$if(natbib)$
{\small\bibliographystyle{$if(biblio-style)$$biblio-style$$else$unsrtnat$endif$}
$if(bibliography)$
\bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
$endif$
$endif$


% See this guide for more information on BibTeX:
% http://libguides.mit.edu/content.php?pid=55482&sid=406343

% For more author guidance please see:
% http://wellcomeopenresearch.org/for-authors/article-guidelines

% When all authors are happy with the paper, use the
% ‘Submit to WELLCOME OPEN RESEARCH' button from the menu above
% to submit directly to the open life science journal Wellcome Open Research.

% Please note that this template results in a draft pre-submission PDF document.
% Articles will be professionally typeset when accepted for publication.

% We hope you find the Wellcome Open Research Overleaf template useful,
% please let us know if you have any feedback using the help menu above.

$for(include-after)$
$include-after$

$endfor$

\end{document}
