feat: solving issue #57

slides/creators/Decorating_the_Workflow.tex

@@ -384,6 +384,28 @@ \subsection{The Configuration File}
   \end{lstlisting}	
 \end{frame} 
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{frame}[fragile]
+  \frametitle{Portable Workflow Configuration without Paths?}
+  \begin{columns}
+  	\begin{column}{0.5\textwidth}
+  	  \includegraphics[width=0.9\textwidth]{filesystem/overview.png}
+  	\end{column}
+    \begin{column}{0.5\textwidth}
+    	\begin{question}
+    		How can we have a configuration file without file system specifics, run our workflow from \altverb{HOME} and still provide or use a workflow, when our data resides \textbf{elsewhere}?
+    	\end{question}
+    \end{column}
+  \end{columns}
+  \pause
+  \Snakemake provides the \altverb{--directory} flag for exactly this purpose. You may run
+  \begin{lstlisting}[language=Bash, style=Shell]
+$ pwd # somewhere /home/.../workflow
+$ snakemake --directory /lustre/project/... # example path
+  \end{lstlisting}
+  \Snakemake will now create and search for all directories relative to \altverb{directory}.
+\end{frame} 
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{The Command Line}