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feat: interlude introducing multiext
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cmeesters committed Feb 7, 2025
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18 changes: 17 additions & 1 deletion slides/common/using_wrappers.tex
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Expand Up @@ -62,7 +62,23 @@ \subsection{Using Wrappers}
\end{docs}
\end{frame}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{frame}[fragile]
\frametitle{\Interlude{Dealing with multiple Extensions}}
\begin{warning}
So far, we were referring to \emph{one} file. But alignment software like \altverb{bwa} requires all those files with multiple extensions! {\bf This is not safe!}
\end{warning}
To require multiple extensions \Snakemake provides the \altverb{multiext()}-function:
\begin{lstlisting}[language=Python,style=Python]
rule bwa_map:
input:
...
idx=multiext("genome", ".amb", ".fa",
".ann", ".bwt", ".pac", ".sa")
...
\end{lstlisting}
Now, \emph{all} listed extensions are required to be present for the file with the prefix \altverb{genome}!
\end{frame}



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