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authorJustin Bedo <cu@cua0.org>2020-12-07 16:30:53 +1100
committerJustin Bedo <cu@cua0.org>2020-12-07 16:30:53 +1100
commit5cf9dcf15c3e384d02b81e81cb3e2c4a1de0efa4 (patch)
tree855679ee656b1f4ea3a155e861347fb8499b29fe /slides.tex
parent0c566119872b385fe3eabef3ab308c02f71d65d2 (diff)
first draft
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-rw-r--r--slides.tex101
1 files changed, 80 insertions, 21 deletions
diff --git a/slides.tex b/slides.tex
index c51f1e5..04ed327 100644
--- a/slides.tex
+++ b/slides.tex
@@ -20,7 +20,7 @@
\author{Justin Bed\H{o}\\WEHI}
\title{\includegraphics[width=.7\linewidth]{logo}\\functional, reproducible bioinformatics workflows}
-\date{November 10, 2020}
+\date{December 8th, 2020}
\begin{document}
@@ -40,7 +40,7 @@
\item More complex than a straight chain
\end{enumerate}
\begin{center}
- $\Rightarrow$ tooling needed for reproducibility
+ $\Rightarrow$ tooling needed for reproducibility\footnote{generate bit-identical output from an analysis specification on any machine with sufficient resources}
\end{center}
\end{frame}
@@ -169,8 +169,6 @@
\begin{minipage}{.55\textwidth}
\begin{overprint}
\onslide<1>\includegraphics[width=\linewidth]{pipeline}
- \onslide<2>\includegraphics[width=.75\linewidth]{bwa-stage}
- \onslide<3>\includegraphics[width=\linewidth]{bwa-drv}
\end{overprint}
\end{minipage}
\end{frame}
@@ -199,30 +197,91 @@
\end{frame}
\begin{frame}
- \frametitle{NextFlow example translation}
- \begin{minipage}{.5\textwidth}
- \begin{block}{BioNix}
- \vspace{.25cm}
- \includegraphics[height=.65\textheight]{nextflow-nix}
- \end{block}
- \end{minipage}
- \begin{minipage}{.4\textwidth}
- \begin{block}{NextFlow}
- \vspace{.25cm}
- \includegraphics[height=.65\textheight]{nextflow}
- \end{block}
- \end{minipage}
+ \frametitle{Stafford Fox Rare Cancer Project}
+ \begin{enumerate}
+ \item $\geq100$ WGS/WES samples totalling 20 TiB of primary data
+ \item Clinical \& research driven
+ \item Timely reporting to requesting clinicians
+ \item Flexibility required to respond to research questions
+ \item Cohort requires consistent processing
+ \item Reproducibility throughout time
+ \end{enumerate}
\end{frame}
\begin{frame}
- \frametitle{Real-world usage at WEHI}
+ \frametitle{Stafford Fox Rare Cancer Project}
\begin{enumerate}
- \item Stafford Fox Rare Cancer Project
- \item $\geq100$ WGS/WES samples totalling 20 TiB of primary data
+ \item Reproducible workflow via BioNix, with version control provided by git
\item SNV calling, neoantigen prediction, structural variants, copy number, mutational signatures, and report generation with embedded revision hash
- \item CI ensures reports are always up to date and consistent across the cohort
+ \item Handles WES, WGS, comprehensive cancer panel, PDX
+ \item Continuous integration ensures reports are always up to date and consistent across the cohort
\item Processed at Pawsey (Slurm) and WEHI (PBS \& Slurm)
+ \item Almost completely automated handling of new data
+ \end{enumerate}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Example report}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Stafford Fox Rare Cancer Workflow}
+ \includegraphics[width=\linewidth]{sfrc01042}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Stafford Fox Rare Cancer Workflow}
+ \includegraphics[width=\linewidth]{sfrc01042-gridss}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Generating expressions for new data}
+ \includegraphics[width=.9\linewidth]{autogen}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Integrating RedCap information reproducibly}
+ \begin{minipage}{.3\textwidth}
+ \includegraphics[width=\linewidth]{redcap}
+ \end{minipage}
+ \begin{minipage}{.68\textwidth}
+ \begin{enumerate}
+ \item Difficult, live database without a release schedule
+ \item Solution: store the relevant annotations in the expressions
+ \item Git version control then also applies to the DB content
+ \item Sync script to update annotations
\end{enumerate}
+ \end{minipage}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Benefits from using BioNix}
+ \begin{enumerate}
+ \item Guarantees a high degree of reproducibility and portability
+ \item Easy to modify workflow and add components
+ \item Small continuous integration implementation
+ \item Inbuilt consistency checking via hash verification
+ \end{enumerate}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Issues with BioNix}
+ \begin{enumerate}
+ \item Steep learning curve
+ \begin{enumerate}
+ \item Nix the language
+ \item BioNix/nixpkgs abstractions
+ \item Stafford Fox workflow particulars
+ \end{enumerate}
+ \item Low discoverability
+ \item Modest collection of bioinformatics software in nixpkgs
+ \item Nix evaluation isn't hermetic (fixed with flakes)
+ \end{enumerate}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Alternative configuration structure}
+ \includegraphics[width=\linewidth]{config}
\end{frame}
\begin{frame}