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fix: line break in exercise for 04
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cmeesters committed Apr 19, 2024
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14 changes: 7 additions & 7 deletions slides/creators/A_First_Workflow_condensed.tex
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Expand Up @@ -401,13 +401,13 @@ \subsection{A first Step or ``Rule''}
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:
...
output:
...
shell:
"samtools sort -T sorted_reads/{wildcards.sample} "
"-O bam {input} > {output}"
input:
...
output:
...
shell:
"samtools sort -T sorted_reads/{wildcards.sample}"
" -O bam {input} > {output}"
\end{lstlisting}
\begin{task}
Please refer to your template \newline \altverb{04_Snakefile} in the tutorial folder and fill in \altverb{input} and \altverb{output}.
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