adaptions for 03 cloze text - not ready

slides/creators/A_First_Workflow.tex

@@ -326,8 +326,17 @@ \subsection{A first Step or ``Rule''}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}[fragile]
-  \frametitle{Further Workflow Decoration}\footnotesize 
-  \texttt{Snakemake} allows generalizing rules by using named wildcards. Simply replace the \altverb{A} in the second input file and in the output file with the wildcard \altverb{\{sample\}}, to yield:
+  \frametitle{\HandsOn{Further Workflow Decoration}}
+  (Usually), experiments consists of more than one input, e.\,g. several replicas might be present.\newline
+  \begin{task}{Introducing the \altverb{sample} Wildcard}
+    \texttt{Snakemake} allows generalizing rules by using named wildcards, too. Simply replace the \altverb{A} in the second input file and in the output file with the wildcard \altverb{\{sample\}}.\newline
+    You may refer to the \pathtoclozure{03_Snakefile} template.
+  \end{task}
+\end{frame}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{frame}[fragile]
+  \frametitle{Further Workflow Decoration -- Solution} 
   \begin{lstlisting}[language=Python,style=Python,basicstyle=\footnotesize]
 rule bwa_map:
     input:
@@ -338,15 +347,10 @@ \subsection{A first Step or ``Rule''}
     shell:
         "bwa mem {input} | samtools view -Sb - > {output}"
   \end{lstlisting}
-  When \texttt{Snakemake} determines that this rule can be applied to generate a target file by replacing the wildcard \altverb{\{sample\}} in the output file with an appropriate value, it will propagate that value to all occurrences of \altverb{\{sample\}} in the input files and thereby determine the necessary input for the resulting job. 
-\end{frame}
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\begin{frame}
-  \frametitle{One Caveat!}
-  \begin{alertblock}{Multiple Wildcards}
-    You can have multiple wildcards in your file paths, however, to avoid conflicts with other jobs of the same rule, \emph{all output files} of a rule \emph{have to contain exactly the same wildcards}.
-  \end{alertblock}
+  \begin{docs}{Background}
+  When \texttt{Snakemake} determines that this rule can be applied to generate a target file by replacing the wildcard \altverb{\{sample\}} in the output file with an appropriate value, it will propagate that value to all occurrences of \altverb{\{sample\}} in the input files and thereby determine the necessary input for the resulting job.\newline
+      \pathtosolution{03_Snakefile}
+  \end{docs}
 \end{frame}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -367,26 +371,48 @@ \subsection{A first Step or ``Rule''}
   \end{lstlisting}
 \end{frame}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{frame}
+  \frametitle{One Caveat!}
+  \begin{alertblock}{Multiple Wildcards}
+    You can have multiple wildcards in your file paths, however, to avoid conflicts with other jobs of the same rule, \emph{all output files} of a rule \emph{have to contain exactly the same wildcards}.
+  \end{alertblock}
+\end{frame}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}[fragile]
   \frametitle{Sorting Alignments}
   For later steps, we need the read alignments in the BAM files to be sorted. This can be achieved with the \lhref{https://www.htslib.org/}{\texttt{samtools}} \altverb{sort} command. We add the following rule beneath the \altverb{bwa_map} rule:
   \begin{lstlisting}[language=Python,style=Python]
 rule samtools_sort:
     input:
-        "mapped_reads/{sample}.bam"
+        ...
     output:
-        "sorted_reads/{sample}.bam"
+        ...
     shell:
         "samtools sort -T sorted_reads/{wildcards.sample} "
         "-O bam {input} > {output}"
   \end{lstlisting}
-  %TODO check cloze text correct?
   \begin{task}
-  	Please refer to your template \altverb{03_Snakefile}.
+  	Please refer to your template \altverb{04_Snakefile}. 
   \end{task}
 \end{frame}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{frame}[fragile]
+  \frametitle{Using Wildcards}
+  \begin{lstlisting}[language=Python,style=Python]
+rule samtools_sort:
+    input:
+        "mapped_reads/{sample}.bam"
+    output:
+        "sorted_reads/{sample}.bam"
+    shell:
+        "samtools sort -T sorted_reads/{wildcards.sample} "
+        "-O bam {input} > {output}"
+  \end{lstlisting}
+\end{frame}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}[fragile]
   \frametitle{Using Wildcards}