From 1462a6c32fb89fec094b9a749457f3145f9eed78 Mon Sep 17 00:00:00 2001
From: Fabian Brand <brand@imbie.meb.uni-bonn.de>
Date: Fri, 15 Dec 2023 14:38:40 +0100
Subject: [PATCH 01/12] feat: Adding slides explaining the setup, usage and
 creation of snakemake wrappers.

This is a first attempt to provide some slides to explain all aspects
of wrappers in some depth.

Refs: #44
---
 slides/Snakemake_HPC_Creators.tex |   2 +-
 slides/Snakemake_HPC_Users.tex    |   5 +-
 slides/common/wrapper.tex         | 140 ++++++++++++++++++++++++++++++
 slides/creators/wrapper.tex       | 136 +++++++++++++++++++++++++++++
 4 files changed, 281 insertions(+), 2 deletions(-)
 create mode 100644 slides/common/wrapper.tex
 create mode 100644 slides/creators/wrapper.tex

diff --git a/slides/Snakemake_HPC_Creators.tex b/slides/Snakemake_HPC_Creators.tex
index c8b46e7..52a2535 100644
--- a/slides/Snakemake_HPC_Creators.tex
+++ b/slides/Snakemake_HPC_Creators.tex
@@ -75,7 +75,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \include{common/Workflow_Parameterization_for_HPC}
 
-
+\include{creators/wrapper}
 
 \end{document}
 
diff --git a/slides/Snakemake_HPC_Users.tex b/slides/Snakemake_HPC_Users.tex
index f83d624..728133b 100644
--- a/slides/Snakemake_HPC_Users.tex
+++ b/slides/Snakemake_HPC_Users.tex
@@ -46,8 +46,11 @@
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \include{common/Reports}    
-      
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %\include{common/Contributing} % TODO: should include reporting issues
+
+\include{common/wrapper}
+
 \end{document}
 
diff --git a/slides/common/wrapper.tex b/slides/common/wrapper.tex
new file mode 100644
index 0000000..6f7a463
--- /dev/null
+++ b/slides/common/wrapper.tex
@@ -0,0 +1,140 @@
+\section{Snakemake Wrappers}
+
+\subsection*{Basics}
+
+\begin{frame}
+    \frametitle{Outline}
+    \begin{columns}[t]
+        \begin{column}{.5\textwidth}
+            \tableofcontents[sections={1-9},currentsection]
+        \end{column}
+        \begin{column}{.5\textwidth}
+            \tableofcontents[sections={10-18},currentsection]
+        \end{column}
+    \end{columns}
+\end{frame}
+
+\begin{frame}
+    \frametitle{What is this about?}
+    \begin{question}[Questions]
+        \begin{itemize}
+            \item What is a snakemake Wrapper?
+            \item How can snakemake wrappers be used to write reproducible workflows?
+        \end{itemize}
+    \end{question}
+    \begin{docs}[Objectives]
+        \begin{enumerate}
+            \item Introduce the concept of snakemake wrappers
+            \item Include snakemake wrappers in your workflows
+            \item Reproducibility of snakemake wrappers
+        \end{enumerate}
+    \end{docs}
+\end{frame}
+
+\begin{frame}{Introduction to Wrappers}
+    For a single tool, Snakemake Wrappers do:
+    \begin{itemize}[<+->]
+        \item Document usage
+        \item Describe the dependencies
+        \item Provide a way to call the tool with information from snakemake
+    \end{itemize}
+    This setup makes snakemake wrappers reusable across multiple workflows.
+\end{frame}
+
+\begin{frame}{Introduction to Wrappers}
+    Wrappers consist of three components:
+    \begin{enumerate}
+        \item A description of their usage (\altverb{meta.yaml})
+        \item A conda environment description of all dependencies of the tool (\altverb{environment.yaml})
+        \item A python script that invokes the tool (\altverb{wrapper.py})
+    \end{enumerate}
+    Since they are reusable, there is a large repository online of tried and tested 
+    wrappers written by the community: \lhref{https://github.com/snakemake/snakemake-wrappers}{snakemake-wrappers}
+\end{frame}
+
+\begin{frame}[fragile]{Using Wrappers}
+    Using snakemake wrappers can be achieved easily:
+    \begin{lstlisting}[language=Python,style=Python]
+rule bwa_map:
+    input:
+        reads=["input/{sample}_1.fq.gz", "input/{sample}_2.fq.gz"],
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
+    output:
+        "output/{sample}.bam"
+    params:
+        extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
+        sorting="none",  # Can be 'none', 'samtools' or 'picard'.
+        sort_order="queryname",  # Can be 'queryname' or 'coordinate'.
+        sort_extra="",  # Extra args for samtools/picard.
+    threads: 8
+    wrapper:
+        "v3.2.0/bio/bwa/mem"
+    \end{lstlisting}
+    \begin{docs}
+        This example uses the community snakemake-wrappers repository \altverb{bwa-mem} wrapper.
+    \end{docs}
+\end{frame}
+
+\begin{frame}[fragile]{Using Wrappers: In- and Output}
+    Input and Output of the rules has to match the definition of the snakemake wrapper.
+    \begin{lstlisting}[language=Python,style=Python]
+rule bwa_map:
+    input:
+        reads=["input/{sample}_1.fq.gz", "input/{sample}_2.fq.gz"],
+        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
+    output:
+        "output/{sample}.bam"
+    ...
+    \end{lstlisting}
+    \begin{docs}
+        The \altverb{bwa-mem} wrapper expects an input object with two attributes
+        \altverb{reads} and \altverb{idx} and writes to a single output file.
+    \end{docs}
+\end{frame}
+
+\begin{frame}[fragile]{Using Wrappers: Parameters}
+    Parameters may be used by wrappers to influence the behaviour, settings or resource usage.
+    \begin{lstlisting}[language=Python,style=Python]
+rule bwa_map:
+    ...
+    params:
+        extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
+        sorting="none",  # Can be 'none', 'samtools' or 'picard'.
+        sort_order="queryname",  # Can be 'queryname' or 'coordinate'.
+        sort_extra="",  # Extra args for samtools/picard.
+    threads: 8
+    ...
+    \end{lstlisting}
+    \begin{docs}
+        \altverb{bwa-mem} supports custom arguments like \altverb{sort_order} and
+        the common \altverb{extra} flag, that is used to supply command line parameters
+        for the invocation of the tool. The \altverb{threads} and \altverb{resources}
+        settings from a snakemake rule are also commonly used to set memory or parallelization
+        parameters for each tool.
+    \end{docs}
+\end{frame}
+
+\begin{frame}[fragile]{Using Wrappers: Calling a Wrapper}
+    The \altverb{wrapper} directive signals that snakemake should execute this rule with
+    a wrapper.
+    \begin{lstlisting}[language=Python,style=Python]
+rule bwa_map:
+    ...
+    wrapper:
+        "v3.2.0/bio/bwa/mem"
+    \end{lstlisting}
+    \begin{docs}
+        The path to the tool is given relative to the repository or path given by the \altverb{--wrapper-prefix}
+        flag, which defaults to the \lhref{https://github.com/snakemake/snakemake-wrappers}{snakemake-wrappers} repository.
+    \end{docs}
+\end{frame}
+
+\begin{frame}{Advantages of Wrappers}
+    Using wrappers has many great advantages compared to \altverb{run} or \altverb{shell}:
+    \begin{itemize}[<+->]
+        \item Code is reusable across workflows and can be shared with others
+        \item Complex invocations of tools do not clutter your snakemake workflow definitions
+        \item With versioned wrappers, you workflow is easily reproducible
+        \item Community wrappers often get you started quickly using a new tool correctly
+    \end{itemize}
+\end{frame}
diff --git a/slides/creators/wrapper.tex b/slides/creators/wrapper.tex
new file mode 100644
index 0000000..f36153e
--- /dev/null
+++ b/slides/creators/wrapper.tex
@@ -0,0 +1,136 @@
+\input{common/wrapper}
+
+\subsection*{Advanced}
+
+\begin{frame}{Creating New Wrappers}
+    Creating snakemake wrappers is as easy as creating the three constituent parts:
+    \begin{description}[<+->]
+        \item[\texttt{meta.yaml}:] A documentation file, containing information about the tool and the wrapper
+        \item[\texttt{environment.yaml}:] A conda environment to install the tool and its dependencies
+        \item[\texttt{wrapper.py}:] The python code to run the tool 
+    \end{description}
+    \only<1>{
+        Contents of the documentation:
+        \begin{itemize}
+            \item The name of the wrapper and the tool it wraps
+            \item Links to the tool source code
+            \item Description of the input and output files that should be supplied by any rule using the wrapper
+            \item Optionally, some documentation of custom arguments like \altverb{extra}
+            \item When contributing to the community: Authors of the wrapper
+        \end{itemize}
+    }
+    \only<2>{
+        Software Environment:
+        \begin{itemize}
+            \item Install all necessary tools and dependencies to run the wrapper code (including python libraries)
+            \item Preferably tool versions should be fixed, s.t. later usage of the same wrapper results in the same output
+        \end{itemize}
+    }
+    \only<3>{
+        The wrapper code:
+        \begin{itemize}
+            \item Translate the snakemake rule parameters into a valid invocation of the tool
+            \item Apply necessary pre- and postprocessing steps to guarantee valid output
+        \end{itemize}
+    }
+    \only<4>{
+        \begin{docs}
+            Wrappers can be improved by providing \altverb{Unit Tests} that can validate the wrapper code
+            and tool versions with known output.
+        \end{docs}
+    }
+\end{frame}
+
+\begin{frame}[fragile]{Creating New Wrappers: Python Code}
+    \altverb{wrapper.py} is the core component of any wrapper as it takes care of running the actual
+    program.
+    \begin{onlyenv}<2>
+        \begin{lstlisting}[language=Python,style=Python,gobble=12]
+            # Core setup of a `wrapper.py` script
+            # 1. Python Imports
+            import tempfile
+            import os
+            from snakemake.shell import shell
+        \end{lstlisting}
+    \end{onlyenv}
+    \begin{onlyenv}<3>
+        \begin{lstlisting}[language=Python,style=Python,gobble=12]
+            # Core setup of a `wrapper.py` script
+            # 2. Fetch the snakemake input and output parameter
+            extra = snakemake.params.get("extra", "")
+        \end{lstlisting}
+        The snakemake object has the attributes \altverb{input}, \altverb{output} and \altverb{params}
+        containing the respective rule parameter.
+    \end{onlyenv}
+    \begin{onlyenv}<4>
+        \begin{lstlisting}[language=Python,style=Python,gobble=12]
+            # Core setup of a `wrapper.py` script
+                                            Default value
+                                                 @vvvv@
+            extra = snakemake.params.get("extra", "")
+                                         @^^^^^^^@
+                                    Name of the parameter
+        \end{lstlisting}
+        The snakemake object has the attributes \altverb{input}, \altverb{output} and \altverb{params}
+        containing the respective rule parameter.
+    \end{onlyenv}
+    \begin{onlyenv}<5>
+        \begin{lstlisting}[language=Python,style=Python,gobble=12]
+            # Core setup of a `wrapper.py` script
+            extra = snakemake.params.get("extra", "")
+            reads = snakemake.input.get("reads", [])
+            output = snakemake.output[0]
+        \end{lstlisting}
+        \begin{itemize}
+            \item These values can also be addressed as arrays
+            \item The wrapper must take care of checking for errors in the input and raise Exceptions if necessary
+        \end{itemize}
+    \end{onlyenv}
+    \begin{hint}
+        The \altverb{snakemake} object provides access to snakemake variables from inside the
+        wrapper script.
+    \end{hint}
+\end{frame}
+
+\begin{frame}[fragile]{Creating New Wrappers: Helper Functions}
+    Snakemake provides several helper functions that make it easier to code wrappers.
+    \begin{lstlisting}[language=Python,style=Python,gobble=8]
+        # Snakemake Helper Functions
+
+        # Run a specific tool on the command line.
+        snakemake.shell("/bin/true")
+
+        # Format the log statement of the current rule, s.t. it can be applied to a shell command.
+        snakemake.log_fmt_shell(stdout=True, stderr=True, append=False)
+
+        # Define the executable used to launch your shell commands.
+        snakemake.shell.executable("/bin/bash")
+    \end{lstlisting}
+\end{frame}
+
+\begin{frame}{Assembling the new Wrapper}
+    With these ingredients, you can write wrappers for your own tools.
+    Recap of the steps required to create a new wrapper:
+    \begin{itemize}
+        \item Pick the tool and write the wrapper
+        \item Test the wrapper and document how to use it
+        \item Optionally, write some unit testing code for the wrapper
+        \item Use it in your workflows
+    \end{itemize}
+    \begin{docs}
+        If you write new wrappers, please contribute them to the community effort.
+    \end{docs}
+\end{frame}
+
+\begin{frame}{Contributing Wrappers to the Community}
+    New wrappers are always welcome at \lhref{https://github.com/snakemake/snakemake-wrappers}{snakemake-wrappers}.
+    In order to contribute a new wrapper, please provide:
+    \begin{itemize}
+        \item A Wrapper, including \altverb{meta.yaml}, \altverb{environment.yaml} and \altverb{wrapper.py}
+        \item A simple unit test with some example data
+    \end{itemize}
+    \begin{hint}
+        Your example serves as the main documentation for the wrapper, so make sure to document
+        the usage of any custom parameters, input and output variables.
+    \end{hint}
+\end{frame}

From 07909c0b7ed75c03149a89433a4a867ea4a0dead Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Wed, 31 Jan 2024 15:24:02 +0100
Subject: [PATCH 02/12] common/wrapper - inserted optical frame separators

---
 slides/common/wrapper.tex | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/slides/common/wrapper.tex b/slides/common/wrapper.tex
index 6f7a463..515ce63 100644
--- a/slides/common/wrapper.tex
+++ b/slides/common/wrapper.tex
@@ -1,7 +1,10 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Snakemake Wrappers}
 
-\subsection*{Basics}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\subsection{Basics}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}
     \frametitle{Outline}
     \begin{columns}[t]
@@ -14,6 +17,7 @@ \subsection*{Basics}
     \end{columns}
 \end{frame}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}
     \frametitle{What is this about?}
     \begin{question}[Questions]
@@ -31,6 +35,7 @@ \subsection*{Basics}
     \end{docs}
 \end{frame}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}{Introduction to Wrappers}
     For a single tool, Snakemake Wrappers do:
     \begin{itemize}[<+->]
@@ -41,6 +46,7 @@ \subsection*{Basics}
     This setup makes snakemake wrappers reusable across multiple workflows.
 \end{frame}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}{Introduction to Wrappers}
     Wrappers consist of three components:
     \begin{enumerate}
@@ -52,6 +58,7 @@ \subsection*{Basics}
     wrappers written by the community: \lhref{https://github.com/snakemake/snakemake-wrappers}{snakemake-wrappers}
 \end{frame}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}[fragile]{Using Wrappers}
     Using snakemake wrappers can be achieved easily:
     \begin{lstlisting}[language=Python,style=Python]
@@ -75,6 +82,7 @@ \subsection*{Basics}
     \end{docs}
 \end{frame}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}[fragile]{Using Wrappers: In- and Output}
     Input and Output of the rules has to match the definition of the snakemake wrapper.
     \begin{lstlisting}[language=Python,style=Python]
@@ -92,6 +100,7 @@ \subsection*{Basics}
     \end{docs}
 \end{frame}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}[fragile]{Using Wrappers: Parameters}
     Parameters may be used by wrappers to influence the behaviour, settings or resource usage.
     \begin{lstlisting}[language=Python,style=Python]
@@ -114,6 +123,7 @@ \subsection*{Basics}
     \end{docs}
 \end{frame}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}[fragile]{Using Wrappers: Calling a Wrapper}
     The \altverb{wrapper} directive signals that snakemake should execute this rule with
     a wrapper.
@@ -129,6 +139,7 @@ \subsection*{Basics}
     \end{docs}
 \end{frame}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}{Advantages of Wrappers}
     Using wrappers has many great advantages compared to \altverb{run} or \altverb{shell}:
     \begin{itemize}[<+->]

From 2cf4d628095c50265ff2169b335167ee6b7977da Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Wed, 31 Jan 2024 15:24:45 +0100
Subject: [PATCH 03/12] moved common/wrapper.tex -> common/using_wrappers.tex

---
 slides/common/{wrapper.tex => using_wrappers.tex} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename slides/common/{wrapper.tex => using_wrappers.tex} (100%)

diff --git a/slides/common/wrapper.tex b/slides/common/using_wrappers.tex
similarity index 100%
rename from slides/common/wrapper.tex
rename to slides/common/using_wrappers.tex

From 6a03db313a8dcdb60c56332cd451272eb3b602e1 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Wed, 31 Jan 2024 15:36:41 +0100
Subject: [PATCH 04/12] Snakemake_HPC_Creators - reflecting name change

---
 slides/Snakemake_HPC_Creators.tex | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/slides/Snakemake_HPC_Creators.tex b/slides/Snakemake_HPC_Creators.tex
index ea99c22..2535c6e 100644
--- a/slides/Snakemake_HPC_Creators.tex
+++ b/slides/Snakemake_HPC_Creators.tex
@@ -72,12 +72,10 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %\include{creators/Uploading_Workflows}
 
-
-
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \include{common/Workflow_Parameterization_for_HPC}
 
-\include{creators/wrapper}
-
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\include{creators/using_wrapper}
 \end{document}
 

From a0fa9d72aaecd3eca2d8853100d8acbec147db32 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Thu, 1 Feb 2024 14:51:54 +0100
Subject: [PATCH 05/12] adapted sections and disentagled tex files for wrappers

---
 slides/Snakemake_HPC_Creators.tex             |  3 +-
 slides/common/HPC_101.tex                     |  4 +-
 slides/common/Plotting_DAGs.tex               |  4 +-
 slides/common/Reports.tex                     |  4 +-
 slides/common/Why_Workflows.tex               |  4 +-
 .../Workflow_Parameterization_for_HPC.tex     |  4 +-
 slides/common/software_environment.tex        |  4 +-
 slides/common/using_wrappers.tex              | 60 +++++++++----------
 slides/creators/A_First_Workflow.tex          |  4 +-
 slides/creators/Decorating_the_Workflow.tex   |  4 +-
 slides/creators/Finishing_and_Execution.tex   |  4 +-
 slides/creators/Getting_Started.tex           |  4 +-
 slides/creators/Python_in_Snakemake.tex       |  4 +-
 slides/creators/Sample_Data.tex               |  4 +-
 .../{wrapper.tex => coding_wrappers.tex}      |  6 +-
 15 files changed, 59 insertions(+), 58 deletions(-)
 rename slides/creators/{wrapper.tex => coding_wrappers.tex} (98%)

diff --git a/slides/Snakemake_HPC_Creators.tex b/slides/Snakemake_HPC_Creators.tex
index 2535c6e..a33f5a3 100644
--- a/slides/Snakemake_HPC_Creators.tex
+++ b/slides/Snakemake_HPC_Creators.tex
@@ -76,6 +76,7 @@
 \include{common/Workflow_Parameterization_for_HPC}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\include{creators/using_wrapper}
+\include{common/using_wrappers}
+\include{creators/coding_wrappers}
 \end{document}
 
diff --git a/slides/common/HPC_101.tex b/slides/common/HPC_101.tex
index e39acb0..ffd0665 100644
--- a/slides/common/HPC_101.tex
+++ b/slides/common/HPC_101.tex
@@ -6,10 +6,10 @@ \section{How does Clustercomputing work?}
     \frametitle{Outline}
     \begin{columns}[t]
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={1-9},currentsection]
+            \tableofcontents[sections={1-7},currentsection]
         \end{column}
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={10-18},currentsection]
+            \tableofcontents[sections={8-15},currentsection]
         \end{column}
     \end{columns}
 \end{frame}
diff --git a/slides/common/Plotting_DAGs.tex b/slides/common/Plotting_DAGs.tex
index 7cb3d17..8a829ac 100644
--- a/slides/common/Plotting_DAGs.tex
+++ b/slides/common/Plotting_DAGs.tex
@@ -6,10 +6,10 @@ \section{Plotting DAGs}
     \frametitle{Outline}
     \begin{columns}[t]
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={1-9},currentsection]
+            \tableofcontents[sections={1-7},currentsection]
         \end{column}
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={10-18},currentsection]
+            \tableofcontents[sections={8-15},currentsection]
         \end{column}
     \end{columns}
 \end{frame}
diff --git a/slides/common/Reports.tex b/slides/common/Reports.tex
index 75cf110..23fff78 100644
--- a/slides/common/Reports.tex
+++ b/slides/common/Reports.tex
@@ -6,10 +6,10 @@ \section{Evaluating Reports}
     \frametitle{Outline}
     \begin{columns}[t]
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={1-9},currentsection]
+            \tableofcontents[sections={1-7},currentsection]
         \end{column}
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={10-18},currentsection]
+            \tableofcontents[sections={8-15},currentsection]
         \end{column}
     \end{columns}
 \end{frame}
diff --git a/slides/common/Why_Workflows.tex b/slides/common/Why_Workflows.tex
index 91367bd..3749f84 100644
--- a/slides/common/Why_Workflows.tex
+++ b/slides/common/Why_Workflows.tex
@@ -6,10 +6,10 @@ \section{Why Workflows}
     \frametitle{Outline}
     \begin{columns}[t]
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={1-9},currentsection]
+            \tableofcontents[sections={1-7},currentsection]
         \end{column}
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={10-18},currentsection]
+            \tableofcontents[sections={8-15},currentsection]
         \end{column}
     \end{columns}
 \end{frame}
diff --git a/slides/common/Workflow_Parameterization_for_HPC.tex b/slides/common/Workflow_Parameterization_for_HPC.tex
index a06a2fe..7aa05e9 100644
--- a/slides/common/Workflow_Parameterization_for_HPC.tex
+++ b/slides/common/Workflow_Parameterization_for_HPC.tex
@@ -6,10 +6,10 @@ \section{Parametizing your Workflow - II}
     \frametitle{Outline}
     \begin{columns}[t]
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={1-9},currentsection]
+            \tableofcontents[sections={1-7},currentsection]
         \end{column}
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={10-18},currentsection]
+            \tableofcontents[sections={8-15},currentsection]
         \end{column}
     \end{columns}
 \end{frame}
diff --git a/slides/common/software_environment.tex b/slides/common/software_environment.tex
index cf24705..fbfaa30 100644
--- a/slides/common/software_environment.tex
+++ b/slides/common/software_environment.tex
@@ -6,10 +6,10 @@ \section{Software Environment}
 	\frametitle{Outline}
 	\begin{columns}[t]
 		\begin{column}{.5\textwidth}
-			\tableofcontents[sections={1-9},currentsection]
+            \tableofcontents[sections={1-7},currentsection]
 		\end{column}
 		\begin{column}{.5\textwidth}
-			\tableofcontents[sections={10-18},currentsection]
+            \tableofcontents[sections={8-15},currentsection]
 		\end{column}
 	\end{columns}
 \end{frame}
diff --git a/slides/common/using_wrappers.tex b/slides/common/using_wrappers.tex
index 515ce63..495c433 100644
--- a/slides/common/using_wrappers.tex
+++ b/slides/common/using_wrappers.tex
@@ -1,22 +1,22 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Snakemake Wrappers}
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{Basics}
-
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}
     \frametitle{Outline}
     \begin{columns}[t]
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={1-9},currentsection]
+            \tableofcontents[sections={1-7},currentsection]
         \end{column}
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={10-18},currentsection]
+            \tableofcontents[sections={8-15},currentsection]
         \end{column}
     \end{columns}
 \end{frame}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\subsection{Basics}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}
     \frametitle{What is this about?}
@@ -124,28 +124,28 @@ \subsection{Basics}
 \end{frame}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\begin{frame}[fragile]{Using Wrappers: Calling a Wrapper}
-    The \altverb{wrapper} directive signals that snakemake should execute this rule with
-    a wrapper.
-    \begin{lstlisting}[language=Python,style=Python]
-rule bwa_map:
-    ...
-    wrapper:
-        "v3.2.0/bio/bwa/mem"
-    \end{lstlisting}
-    \begin{docs}
-        The path to the tool is given relative to the repository or path given by the \altverb{--wrapper-prefix}
-        flag, which defaults to the \lhref{https://github.com/snakemake/snakemake-wrappers}{snakemake-wrappers} repository.
-    \end{docs}
-\end{frame}
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\begin{frame}{Advantages of Wrappers}
-    Using wrappers has many great advantages compared to \altverb{run} or \altverb{shell}:
-    \begin{itemize}[<+->]
-        \item Code is reusable across workflows and can be shared with others
-        \item Complex invocations of tools do not clutter your snakemake workflow definitions
-        \item With versioned wrappers, you workflow is easily reproducible
-        \item Community wrappers often get you started quickly using a new tool correctly
-    \end{itemize}
-\end{frame}
+% \begin{frame}[fragile]{Using Wrappers: Calling a Wrapper}
+%     The \altverb{wrapper} directive signals that snakemake should execute this rule with
+%     a wrapper.
+%     \begin{lstlisting}[language=Python,style=Python]
+% rule bwa_map:
+%     ...
+%     wrapper:
+%         "v3.2.0/bio/bwa/mem"
+%     \end{lstlisting}
+%     \begin{docs}
+%         The path to the tool is given relative to the repository or path given by the \altverb{--wrapper-prefix}
+%         flag, which defaults to the \lhref{https://github.com/snakemake/snakemake-wrappers}{snakemake-wrappers} repository.
+%     \end{docs}
+% \end{frame}
+% 
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% \begin{frame}{Advantages of Wrappers}
+%     Using wrappers has many great advantages compared to \altverb{run} or \altverb{shell}:
+%     \begin{itemize}[<+->]
+%         \item Code is reusable across workflows and can be shared with others
+%         \item Complex invocations of tools do not clutter your snakemake workflow definitions
+%         \item With versioned wrappers, you workflow is easily reproducible
+%         \item Community wrappers often get you started quickly using a new tool correctly
+%     \end{itemize}
+% \end{frame}
diff --git a/slides/creators/A_First_Workflow.tex b/slides/creators/A_First_Workflow.tex
index fddec47..a61bb7e 100644
--- a/slides/creators/A_First_Workflow.tex
+++ b/slides/creators/A_First_Workflow.tex
@@ -6,10 +6,10 @@ \section{A first Workflow}
     \frametitle{Outline}
     \begin{columns}[t]
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={1-9},currentsection]
+            \tableofcontents[sections={1-7},currentsection]
         \end{column}
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={10-18},currentsection]
+            \tableofcontents[sections={8-15},currentsection]
         \end{column}
     \end{columns}
 \end{frame}
diff --git a/slides/creators/Decorating_the_Workflow.tex b/slides/creators/Decorating_the_Workflow.tex
index 6482583..7cb83b0 100644
--- a/slides/creators/Decorating_the_Workflow.tex
+++ b/slides/creators/Decorating_the_Workflow.tex
@@ -6,10 +6,10 @@ \section{Decorating Workflows - Parameterization}
     \frametitle{Outline}
     \begin{columns}[t]
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={1-9},currentsection]
+            \tableofcontents[sections={1-7},currentsection]
         \end{column}
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={10-18},currentsection]
+            \tableofcontents[sections={8-15},currentsection]
         \end{column}
     \end{columns}
 \end{frame}
diff --git a/slides/creators/Finishing_and_Execution.tex b/slides/creators/Finishing_and_Execution.tex
index c8dfcbd..ed9a459 100644
--- a/slides/creators/Finishing_and_Execution.tex
+++ b/slides/creators/Finishing_and_Execution.tex
@@ -6,10 +6,10 @@ \section{Finishing and Executing the Workflow}
     \frametitle{Outline}
     \begin{columns}[t]
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={1-9},currentsection]
+            \tableofcontents[sections={1-7},currentsection]
         \end{column}
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={10-18},currentsection]
+            \tableofcontents[sections={8-15},currentsection]
         \end{column}
     \end{columns}
 \end{frame}
diff --git a/slides/creators/Getting_Started.tex b/slides/creators/Getting_Started.tex
index 4deb512..9455286 100644
--- a/slides/creators/Getting_Started.tex
+++ b/slides/creators/Getting_Started.tex
@@ -6,10 +6,10 @@ \section{Getting Started with Snakemake}
     \frametitle{Outline}
     \begin{columns}[t]
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={1-9},currentsection]
+            \tableofcontents[sections={1-7},currentsection]
         \end{column}
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={10-18},currentsection]
+            \tableofcontents[sections={8-15},currentsection]
         \end{column}
     \end{columns}
 \end{frame}
diff --git a/slides/creators/Python_in_Snakemake.tex b/slides/creators/Python_in_Snakemake.tex
index 660a9d6..afe1a59 100644
--- a/slides/creators/Python_in_Snakemake.tex
+++ b/slides/creators/Python_in_Snakemake.tex
@@ -6,10 +6,10 @@ \section{Snakefiles as Python-Code}
     \frametitle{Outline}
     \begin{columns}[t]
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={1-9},currentsection]
+            \tableofcontents[sections={1-7},currentsection]
         \end{column}
         \begin{column}{.5\textwidth}
-            \tableofcontents[sections={10-18},currentsection]
+            \tableofcontents[sections={8-15},currentsection]
         \end{column}
     \end{columns}
 \end{frame}
diff --git a/slides/creators/Sample_Data.tex b/slides/creators/Sample_Data.tex
index af1a325..a943d10 100644
--- a/slides/creators/Sample_Data.tex
+++ b/slides/creators/Sample_Data.tex
@@ -6,10 +6,10 @@ \section{Getting your Sample Data}
 	\frametitle{Outline}
 	\begin{columns}[t]
 		\begin{column}{.5\textwidth}
-			\tableofcontents[sections={1-9},currentsection]
+            \tableofcontents[sections={1-7},currentsection]
 		\end{column}
 		\begin{column}{.5\textwidth}
-			\tableofcontents[sections={10-18},currentsection]
+            \tableofcontents[sections={8-15},currentsection]
 		\end{column}
 	\end{columns}
 \end{frame}
diff --git a/slides/creators/wrapper.tex b/slides/creators/coding_wrappers.tex
similarity index 98%
rename from slides/creators/wrapper.tex
rename to slides/creators/coding_wrappers.tex
index f36153e..ae549bb 100644
--- a/slides/creators/wrapper.tex
+++ b/slides/creators/coding_wrappers.tex
@@ -1,8 +1,8 @@
-\input{common/wrapper}
 
-\subsection*{Advanced}
 
-\begin{frame}{Creating New Wrappers}
+\section{Coding own Wrappers}
+
+\begin{frame}{Creating new Wrappers}
     Creating snakemake wrappers is as easy as creating the three constituent parts:
     \begin{description}[<+->]
         \item[\texttt{meta.yaml}:] A documentation file, containing information about the tool and the wrapper

From c1a7372b21390ff30408e0bd10ed327a4e107bc0 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Thu, 1 Feb 2024 15:37:13 +0100
Subject: [PATCH 06/12] common/using_wrappers - introduced consistent usage of
 the Snakemake layout

---
 slides/common/using_wrappers.tex | 74 ++++++++++++++++----------------
 1 file changed, 37 insertions(+), 37 deletions(-)

diff --git a/slides/common/using_wrappers.tex b/slides/common/using_wrappers.tex
index 495c433..644ed9e 100644
--- a/slides/common/using_wrappers.tex
+++ b/slides/common/using_wrappers.tex
@@ -15,35 +15,35 @@ \section{Snakemake Wrappers}
 \end{frame}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{Basics}
+\subsection{Using Wrappers}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}
     \frametitle{What is this about?}
     \begin{question}[Questions]
         \begin{itemize}
-            \item What is a snakemake Wrapper?
-            \item How can snakemake wrappers be used to write reproducible workflows?
+            \item What is a Snakemake Wrapper?
+            \item How can Snakemake wrappers be used to write reproducible workflows?
         \end{itemize}
     \end{question}
     \begin{docs}[Objectives]
         \begin{enumerate}
-            \item Introduce the concept of snakemake wrappers
-            \item Include snakemake wrappers in your workflows
-            \item Reproducibility of snakemake wrappers
+            \item Introduce the concept of Snakemake wrappers
+            \item Include Snakemake wrappers in your workflows
+            \item Reproducibility of Snakemake wrappers
         \end{enumerate}
     \end{docs}
 \end{frame}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}{Introduction to Wrappers}
-    For a single tool, Snakemake Wrappers do:
+    For a single tool, \Snakemake{} Wrappers do:
     \begin{itemize}[<+->]
         \item Document usage
         \item Describe the dependencies
-        \item Provide a way to call the tool with information from snakemake
+        \item Provide a way to call the tool with information from Snakemake
     \end{itemize}
-    This setup makes snakemake wrappers reusable across multiple workflows.
+    This setup makes Snakemake wrappers reusable across multiple workflows.
 \end{frame}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -60,7 +60,7 @@ \subsection{Basics}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}[fragile]{Using Wrappers}
-    Using snakemake wrappers can be achieved easily:
+    Using \Snakemake{} wrappers can be achieved easily:
     \begin{lstlisting}[language=Python,style=Python]
 rule bwa_map:
     input:
@@ -78,7 +78,7 @@ \subsection{Basics}
         "v3.2.0/bio/bwa/mem"
     \end{lstlisting}
     \begin{docs}
-        This example uses the community snakemake-wrappers repository \altverb{bwa-mem} wrapper.
+        This example uses the community Snakemake wrappers repository \altverb{bwa-mem} wrapper.
     \end{docs}
 \end{frame}
 
@@ -118,34 +118,34 @@ \subsection{Basics}
         \altverb{bwa-mem} supports custom arguments like \altverb{sort_order} and
         the common \altverb{extra} flag, that is used to supply command line parameters
         for the invocation of the tool. The \altverb{threads} and \altverb{resources}
-        settings from a snakemake rule are also commonly used to set memory or parallelization
+        settings from a Snakemake rule are also commonly used to set memory or parallelization
         parameters for each tool.
     \end{docs}
 \end{frame}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% \begin{frame}[fragile]{Using Wrappers: Calling a Wrapper}
-%     The \altverb{wrapper} directive signals that snakemake should execute this rule with
-%     a wrapper.
-%     \begin{lstlisting}[language=Python,style=Python]
-% rule bwa_map:
-%     ...
-%     wrapper:
-%         "v3.2.0/bio/bwa/mem"
-%     \end{lstlisting}
-%     \begin{docs}
-%         The path to the tool is given relative to the repository or path given by the \altverb{--wrapper-prefix}
-%         flag, which defaults to the \lhref{https://github.com/snakemake/snakemake-wrappers}{snakemake-wrappers} repository.
-%     \end{docs}
-% \end{frame}
-% 
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% \begin{frame}{Advantages of Wrappers}
-%     Using wrappers has many great advantages compared to \altverb{run} or \altverb{shell}:
-%     \begin{itemize}[<+->]
-%         \item Code is reusable across workflows and can be shared with others
-%         \item Complex invocations of tools do not clutter your snakemake workflow definitions
-%         \item With versioned wrappers, you workflow is easily reproducible
-%         \item Community wrappers often get you started quickly using a new tool correctly
-%     \end{itemize}
-% \end{frame}
+ \begin{frame}[fragile]{Using Wrappers: Calling a Wrapper}
+     The \altverb{wrapper} directive signals that \Snakemake{} should execute this rule with
+     a wrapper.
+     \begin{lstlisting}[language=Python,style=Python]
+ rule bwa_map:
+     ...
+     wrapper:
+         "v3.2.0/bio/bwa/mem"
+     \end{lstlisting}
+     \begin{docs}
+         The path to the tool is given relative to the repository or path given by the \altverb{--wrapper-prefix}
+         flag, which defaults to the \lhref{https://github.com/snakemake/snakemake-wrappers}{snakemake-wrappers} repository.
+     \end{docs}
+ \end{frame}
+ 
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ \begin{frame}{Advantages of Wrappers}
+     Using wrappers has many great advantages compared to \altverb{run} or \altverb{shell}:
+     \begin{itemize}[<+->]
+         \item Code is reusable across workflows and can be shared with others
+         \item Complex invocations of tools do not clutter your \Snakemake{} workflow definitions
+         \item With versioned wrappers, you workflow is easily reproducible
+         \item Community wrappers often get you started quickly using a new tool correctly
+     \end{itemize}
+ \end{frame}

From 3fe7f2b520c06250870297c883aa385048290038 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Thu, 1 Feb 2024 15:37:41 +0100
Subject: [PATCH 07/12] adapt_sections.py - will silently ignore configured tex
 files

---
 slides/adapt_sections.py | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/slides/adapt_sections.py b/slides/adapt_sections.py
index 853f5e7..b344b60 100755
--- a/slides/adapt_sections.py
+++ b/slides/adapt_sections.py
@@ -49,8 +49,11 @@ def count_matching_lines(fp):
 def count_sections(file_list):
     count = 0
     for fname in file_list:
-        with open(fname) as fp:
-            count += count_matching_lines(fp)
+        try:
+            with open(fname) as fp:
+               count += count_matching_lines(fp)
+        except:
+            print(f"Error treating: '{fname}'")
     return count
 
 def define_boundaries(section_count):
@@ -62,8 +65,12 @@ def define_boundaries(section_count):
 
 def find_and_replace(boundaries, fname):
     # tex files aren't big, read all content in memory
-    with open(fname) as infile:
-        lines = infile.readlines()
+    try:
+        with open(fname) as infile:
+            lines = infile.readlines()
+    except:
+        print(f"Error treating: '{fname}'")
+        return
 
     # get the matching 'currentsection' lines
     first_done, second_done = False, False

From ef6c3fec448ef0117ef50d7ad769800106100ac3 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Thu, 1 Feb 2024 15:44:27 +0100
Subject: [PATCH 08/12] common/using_wrappers - changed wrapper doc URL to
 readthedocs-link

---
 slides/common/using_wrappers.tex | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/slides/common/using_wrappers.tex b/slides/common/using_wrappers.tex
index 644ed9e..c812049 100644
--- a/slides/common/using_wrappers.tex
+++ b/slides/common/using_wrappers.tex
@@ -22,15 +22,15 @@ \subsection{Using Wrappers}
     \frametitle{What is this about?}
     \begin{question}[Questions]
         \begin{itemize}
-            \item What is a Snakemake Wrapper?
-            \item How can Snakemake wrappers be used to write reproducible workflows?
+            \item What is a \Snakemake{} Wrapper?
+            \item How can \Snakemake{} wrappers be used to write reproducible workflows?
         \end{itemize}
     \end{question}
     \begin{docs}[Objectives]
         \begin{enumerate}
-            \item Introduce the concept of Snakemake wrappers
-            \item Include Snakemake wrappers in your workflows
-            \item Reproducibility of Snakemake wrappers
+            \item Introduce the concept of \Snakemake{} wrappers
+            \item Include \Snakemake{} wrappers in your workflows
+            \item Reproducibility of \Snakemake{} wrappers
         \end{enumerate}
     \end{docs}
 \end{frame}
@@ -55,7 +55,7 @@ \subsection{Using Wrappers}
         \item A python script that invokes the tool (\altverb{wrapper.py})
     \end{enumerate}
     Since they are reusable, there is a large repository online of tried and tested 
-    wrappers written by the community: \lhref{https://github.com/snakemake/snakemake-wrappers}{snakemake-wrappers}
+    wrappers written by the community: \lhref{https://snakemake-wrappers.readthedocs.io}{snakemake-wrappers}.
 \end{frame}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

From e91a9312991e22227791b6218bd1f077d2f5652d Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Thu, 1 Feb 2024 17:28:51 +0100
Subject: [PATCH 09/12] common/using_wrappers - re-arragned and corrected
 layout - better didactics?

---
 slides/common/using_wrappers.tex | 94 ++++++++++++++++++++------------
 1 file changed, 60 insertions(+), 34 deletions(-)

diff --git a/slides/common/using_wrappers.tex b/slides/common/using_wrappers.tex
index c812049..ea5edb7 100644
--- a/slides/common/using_wrappers.tex
+++ b/slides/common/using_wrappers.tex
@@ -58,52 +58,95 @@ \subsection{Using Wrappers}
     wrappers written by the community: \lhref{https://snakemake-wrappers.readthedocs.io}{snakemake-wrappers}.
 \end{frame}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{frame}[fragile]{Using Wrappers - The Example}
+	\begin{docs}
+		The following example uses the \altverb{bwa-mem} wrapper from the \Snakemake-community wrappers repository. The example is specific and let us illustrate the usage.
+		We will cover the usage step by step and specifically:
+		\begin{itemize}
+			\item How to find a wrapper?
+			\item How to use a wrapper.
+		\end{itemize}
+	\end{docs}
+\end{frame}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}[fragile]{Using Wrappers}
-    Using \Snakemake{} wrappers can be achieved easily:
-    \begin{lstlisting}[language=Python,style=Python]
+    Using \Snakemake{} wrappers ease your life as a workflow programmer:
+    \begin{lstlisting}[language=Python,style=Python,basicstyle=\footnotesize]
 rule bwa_map:
     input:
-        reads=["input/{sample}_1.fq.gz", "input/{sample}_2.fq.gz"],
-        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
+        reads=["input/{sample}_1.fq.gz", 
+               "input/{sample}_2.fq.gz"],
+        idx=multiext("genome", ".amb", 
+                 ".ann", ".bwt", ".pac", ".sa"),
     output:
         "output/{sample}.bam"
     params:
         extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
-        sorting="none",  # Can be 'none', 'samtools' or 'picard'.
-        sort_order="queryname",  # Can be 'queryname' or 'coordinate'.
-        sort_extra="",  # Extra args for samtools/picard.
+        sorting="none",  
+        sort_order="queryname",  
+        sort_extra="", 
     threads: 8
     wrapper:
         "v3.2.0/bio/bwa/mem"
     \end{lstlisting}
-    \begin{docs}
-        This example uses the community Snakemake wrappers repository \altverb{bwa-mem} wrapper.
-    \end{docs}
+\end{frame}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{frame}[fragile]{Using Wrappers: Calling a Wrapper}
+	The \altverb{wrapper} directive signals that \Snakemake{} should execute this rule with
+	a wrapper.
+	\begin{lstlisting}[language=Python,style=Python,basicstyle=\small]
+rule bwa_map:
+	...
+	@wrapper:@
+		@"v3.2.0/bio/bwa/mem"@
+	\end{lstlisting}
+	\begin{docs}
+		\begin{columns}
+			\begin{column}{0.5\textwidth}
+				Here, we instruct the code to run with the \altverb{wrapper}-directive.
+				It specifies 
+				\begin{itemize}
+					\item a version
+					\item a directory
+					\item and selects a tool.
+				\end{itemize}
+			\end{column}
+			\begin{column}{0.5\textwidth}\pause
+				The path to the tool is given relative to the workflow or a path given by the \altverb{--wrapper-prefix}
+				flag. By default \Snakemake automatically downloads wrappers from the  \lhref{https://github.com/snakemake/snakemake-wrappers}{wrappers} repository.
+		    \end{column}	
+		\end{columns}
+	\end{docs}
 \end{frame}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}[fragile]{Using Wrappers: In- and Output}
-    Input and Output of the rules has to match the definition of the snakemake wrapper.
-    \begin{lstlisting}[language=Python,style=Python]
+    \altverb{input} and \altverb{output} of the rules has to match the definition of the wrapper:
+    \begin{lstlisting}[language=Python,style=Python,basicstyle=\tiny]
 rule bwa_map:
     input:
-        reads=["input/{sample}_1.fq.gz", "input/{sample}_2.fq.gz"],
-        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
+        reads=["input/{sample}_1.fq.gz", 
+               "input/{sample}_2.fq.gz"],
+        idx=multiext("genome", ".amb", ".ann", 
+                     ".bwt", ".pac", ".sa"),
     output:
         "output/{sample}.bam"
     ...
     \end{lstlisting}
     \begin{docs}
         The \altverb{bwa-mem} wrapper expects an input object with two attributes
-        \altverb{reads} and \altverb{idx} and writes to a single output file.
+        \altverb{reads} and \altverb{idx} and writes to a single output file.\newline
+        The example builds on short reads (hence: 2 inputs) and the \altverb{multiext}-directive allows samples to have multiple different extensions.
     \end{docs}
 \end{frame}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}[fragile]{Using Wrappers: Parameters}
     Parameters may be used by wrappers to influence the behaviour, settings or resource usage.
-    \begin{lstlisting}[language=Python,style=Python]
+    \begin{lstlisting}[language=Python,style=Python,basicstyle=\tiny]
 rule bwa_map:
     ...
     params:
@@ -118,26 +161,9 @@ \subsection{Using Wrappers}
         \altverb{bwa-mem} supports custom arguments like \altverb{sort_order} and
         the common \altverb{extra} flag, that is used to supply command line parameters
         for the invocation of the tool. The \altverb{threads} and \altverb{resources}
-        settings from a Snakemake rule are also commonly used to set memory or parallelization
-        parameters for each tool.
+        settings from a Snakemake rule are also commonly used to set memory or parallelization parameters for each tool.
     \end{docs}
 \end{frame}
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
- \begin{frame}[fragile]{Using Wrappers: Calling a Wrapper}
-     The \altverb{wrapper} directive signals that \Snakemake{} should execute this rule with
-     a wrapper.
-     \begin{lstlisting}[language=Python,style=Python]
- rule bwa_map:
-     ...
-     wrapper:
-         "v3.2.0/bio/bwa/mem"
-     \end{lstlisting}
-     \begin{docs}
-         The path to the tool is given relative to the repository or path given by the \altverb{--wrapper-prefix}
-         flag, which defaults to the \lhref{https://github.com/snakemake/snakemake-wrappers}{snakemake-wrappers} repository.
-     \end{docs}
- \end{frame}
  
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  \begin{frame}{Advantages of Wrappers}

From 37c6fbfc7ffb6acfae17dd12ccd277e26b61b991 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Thu, 1 Feb 2024 17:29:31 +0100
Subject: [PATCH 10/12] Snakemake_HPC_Creators - including using and coding
 wrappers

---
 slides/Snakemake_HPC_Creators.tex | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/slides/Snakemake_HPC_Creators.tex b/slides/Snakemake_HPC_Creators.tex
index a33f5a3..dab41e9 100644
--- a/slides/Snakemake_HPC_Creators.tex
+++ b/slides/Snakemake_HPC_Creators.tex
@@ -77,6 +77,8 @@
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \include{common/using_wrappers}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \include{creators/coding_wrappers}
 \end{document}
 

From 92d4ca9c9ef48657094290d6cebb52dd682a4be7 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Thu, 1 Feb 2024 17:31:04 +0100
Subject: [PATCH 11/12] creators/coding_wrappers - added frame separators

---
 slides/creators/coding_wrappers.tex | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/slides/creators/coding_wrappers.tex b/slides/creators/coding_wrappers.tex
index ae549bb..5747f63 100644
--- a/slides/creators/coding_wrappers.tex
+++ b/slides/creators/coding_wrappers.tex
@@ -1,7 +1,7 @@
-
-
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Coding own Wrappers}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}{Creating new Wrappers}
     Creating snakemake wrappers is as easy as creating the three constituent parts:
     \begin{description}[<+->]
@@ -41,6 +41,7 @@ \section{Coding own Wrappers}
     }
 \end{frame}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}[fragile]{Creating New Wrappers: Python Code}
     \altverb{wrapper.py} is the core component of any wrapper as it takes care of running the actual
     program.
@@ -92,6 +93,7 @@ \section{Coding own Wrappers}
     \end{hint}
 \end{frame}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}[fragile]{Creating New Wrappers: Helper Functions}
     Snakemake provides several helper functions that make it easier to code wrappers.
     \begin{lstlisting}[language=Python,style=Python,gobble=8]
@@ -108,6 +110,7 @@ \section{Coding own Wrappers}
     \end{lstlisting}
 \end{frame}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}{Assembling the new Wrapper}
     With these ingredients, you can write wrappers for your own tools.
     Recap of the steps required to create a new wrapper:
@@ -122,6 +125,7 @@ \section{Coding own Wrappers}
     \end{docs}
 \end{frame}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{frame}{Contributing Wrappers to the Community}
     New wrappers are always welcome at \lhref{https://github.com/snakemake/snakemake-wrappers}{snakemake-wrappers}.
     In order to contribute a new wrapper, please provide:

From f02335cf04f793ab30ecbff4c7a6bda5e4f548dd Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Fri, 2 Feb 2024 11:05:06 +0100
Subject: [PATCH 12/12] Snakemake_HPC_Creators.tex - outcommented the creation
 of wrappers - too much for this course

---
 slides/Snakemake_HPC_Creators.tex | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/slides/Snakemake_HPC_Creators.tex b/slides/Snakemake_HPC_Creators.tex
index dab41e9..362e866 100644
--- a/slides/Snakemake_HPC_Creators.tex
+++ b/slides/Snakemake_HPC_Creators.tex
@@ -79,6 +79,6 @@
 \include{common/using_wrappers}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\include{creators/coding_wrappers}
+%\include{creators/coding_wrappers}
 \end{document}