\documentclass[12pt,a4paper,oneside,captions=tableheading,headinclude,footinclude]{scrartcl} % or twoside
\usepackage[top=25mm,bottom=25mm,left=25mm,right=25mm,head=25pt]{geometry}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage[english,ngerman]{babel}
\usepackage{graphicx}
\usepackage[]{hyperref} % colorlinks, linkcolor = red, citecolor = green, filecolor = black, urlcolor = blue
\usepackage{amsmath}
%\usepackage{biblatex}
\usepackage{siunitx}
\usepackage{caption}
\usepackage{subcaption}
\usepackage{lmodern}
\usepackage{listings}
\usepackage{color}
\usepackage{float}
\usepackage{times}
\usepackage[LGRgreek]{mathastext}
\usepackage{siunitx} 
\usepackage[numbers,square]{natbib}
\usepackage{needspace}
%\usepackage{fancyhdr}
\usepackage[autooneside=false,headsepline,markcase=noupper]{scrlayer-scrpage}
\usepackage{booktabs}
\usepackage{thmbox}
\usepackage{tikz}
\usepackage{lipsum}
\usepackage{wrapfig}
%\usepackage{amssymb}
\usepackage{marginnote}
\usepackage[xindy,nopostdot,symbols,nonumberlist,section=subsection]{glossaries}
\usepackage{glossary-mcols}
\usepackage{chngcntr}
\usepackage{silence}
\WarningFilter{glossaries}{Deprecated command} % To disable some weird warnings that i don't understand
\WarningFilter{mathastext}{current meaning of amsmath}
\usepackage{setspace}
\setstretch{1,5} % this is for 1.5-times line stretching like in Word
%\onehalfspacing % does only multiply the spacing between lines by 1.5, its not a full line stretch!
\setlength{\footheight}{30pt}
\pdfoutput=1
\hypersetup{
    colorlinks=true,
    linkcolor=black,
    citecolor=black,
    filecolor=black,
    urlcolor=black,
}
\renewcommand{\familydefault}{\sfdefault}
\title{Bachelor thesis}
  \subtitle{Upscaling the extracellular glucose oxidase production in \textit{Aspergillus niger} var \textit{tubingensis} strain Ed8}
  \author{Thomas Welter}
  \date{09/12/2016}
\input{commands}
%%% Inserting the complete glossary management
\newglossary[slg]{symb}{syi}{syg}{Units}
\newglossary[mlg]{subs}{tyi}{tyg}{Substances / Mediums}
\newglossary[nlg]{sons}{uyi}{uyg}{Other Abbreviations}
\input{acronyms}
\makeglossaries 
\begin{document}
\selectlanguage{english}
  \input{titlepage}
  
  \pagestyle{scrheadings}
  \clearscrheadfoot
  \KOMAoption{headsepline}{false} 
  \pagenumbering{Roman}
  \setcounter{page}{1}
  \ofoot[\pagemark]{\normalfont\normalcolor\pagemark}
  %\pagestyle{plain}
  \inp{acknowledgements}\clearpage
  \inp{declaration} \clearpage
%%% the obligatory first pages of a thesis
  \setcounter{tocdepth}{2}
  \tableofcontents\clearpage
  \listoffigures\addcontentsline{toc}{section}{List of Figures} \vspace*{-0.5\baselineskip}
  \listoftables\addcontentsline{toc}{section}{List of Tables} \clearpage
  \section*{Abbreviations}\addcontentsline{toc}{section}{Abbreviations} 
  %\glsaddall % for seeing all glossary entries
  \setstretch{1,0}
  \printglossary[style=mystyle,type=symb]
  \printglossary[style=mystyle,type=subs]
  \printglossary[style=mystyle,type=sons]
  \printglossary
  \setstretch{1,5}
  \clearpage
  \automark[subsection]{section}
  \pagestyle{scrheadings}
  \KOMAoption{headsepline}{true} 
  \clearscrheadfoot
  \ofoot[\pagemark]{\normalfont\normalcolor\pagemark}
  %chead{\ifstr{\rightbotmark}{\leftmark}{}{\rightbotmark}} % Display the current subsection
  \chead{\leftmark} % Display the current section
  
%%% main part of the thesis
  \pagenumbering{arabic}
  
  \inp{1_task}
  \inp{2_timeline}
  \inp{3_intro}
  \inp{4_methods}
  \inp{5_results}
  \inp{6_discussion}
  \inp{7_conclusion}
  \clearpage
  
  \pagestyle{scrheadings}
  \clearscrheadfoot
  \KOMAoption{headsepline}{false} 
  \pagenumbering{Roman}
  \setcounter{page}{8}
  \ofoot[\pagemark]{\normalfont\normalcolor\pagemark}
  
%%% references
  %\nocite{*} % for seeing all bibliography entries
  \addcontentsline{toc}{section}{References}
  \bibliographystyle{IEEEtran} % or unsrtnat
  \bibliography{references}{}
  
\end{document}