diff --git a/slides/creators/Decorating_the_Workflow.tex b/slides/creators/Decorating_the_Workflow.tex index 247261e..9150e9f 100644 --- a/slides/creators/Decorating_the_Workflow.tex +++ b/slides/creators/Decorating_the_Workflow.tex @@ -490,6 +490,43 @@ \subsection{The Command Line} \end{itemize} \end{frame} + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +\begin{frame}[fragile] + \frametitle{The \Snakemake{} \texttt{resources} Section} + \Snakemake{} rules provide an additional \altverb{resources} section: + \begin{lstlisting}[language=Python,style=Python] +rule : + ... + resources: + partition='parallel', + mem_mb=1800, + cpus_per_task=4 + \end{lstlisting} + \begin{hint} + Note the \textbf{,}! + \end{hint} + \pause + \begin{docs} + You \emph{may} define \emph{any} resource keyword within any rule. + \end{docs} +\end{frame} + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +\begin{frame} + \frametitle{The \Snakemake{} \texttt{resources} Section - its Downside} + \begin{block}{Every Resource Spec needs a Change per Rule???} + You might have noticed, this specification per rule is most untidy. \Snakemake's design principle is: ship workflows which run \emph{everywhere} \& \emph{every time}. + \newline \pause + Relax: Every bit we can specify: + \begin{itemize} + \item in a \altverb{Snakefile}, + \item on the command line, + \item and re-usable in configuration files! + \end{itemize} + \end{block} +\end{frame} + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{frame}[fragile] \frametitle{Cluster Configuration} @@ -528,43 +565,6 @@ \subsection{The Command Line} \end{question} \end{frame} - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\begin{frame}[fragile] - \frametitle{The \Snakemake{} \texttt{resources} Section} - \Snakemake{} rules provide an additional \altverb{resources} section: - \begin{lstlisting}[language=Python,style=Python] -rule : - ... - resources: - partition='parallel', - mem_mb=1800, - cpus_per_task=4 - \end{lstlisting} - \begin{hint} - Note the \textbf{,}! - \end{hint} - \pause - \begin{docs} - You \emph{may} define \emph{any} resource keyword within any rule. - \end{docs} -\end{frame} - -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\begin{frame} - \frametitle{The \Snakemake{} \texttt{resources} Section - its Downside} - \begin{block}{Every Resource Spec needs a Change per Rule???} - You might have noticed, this specification per rule is most untidy. \Snakemake's design principle is: ship workflows which run \emph{everywhere} \& \emph{every time}. - \newline \pause - Relax: Every bit we can specify: - \begin{itemize} - \item in a \altverb{Snakefile}, - \item on the command line, - \item and re-usable in configuration files! - \end{itemize} - \end{block} -\end{frame} - %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{frame}[fragile] \frametitle{Local Rules}