From 2d7d9dab72268041abaf79d2c7efeddd3a227dcd Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Thu, 25 Apr 2024 12:00:16 +0200 Subject: [PATCH] feat: solving issue #57 --- slides/creators/Decorating_the_Workflow.tex | 22 +++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/slides/creators/Decorating_the_Workflow.tex b/slides/creators/Decorating_the_Workflow.tex index 9150e9f..d0daceb 100644 --- a/slides/creators/Decorating_the_Workflow.tex +++ b/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}