# Creating Workflow Vignettes

## What is a workflow vignette?

Workflow vignettes are documents which describe a bioinformatics workflow that involves multiple Bioconductor packages. These workflows are usually more extensive than the vignettes that accompany individual Bioconductor packages.

Existing Workflow Vignettes

Workflow vignettes may deal with larger data sets and/or be more computationally intensive than typical Bioconductor package vignettes. For this reason, the automated builder that produces these vignettes does not have a time limit (in contrast to the Bioconductor package building system which will time out if package building takes too long).

## Who should write a workflow vignette?

Anyone who is a bioinformatics domain expert.

## How do I write a workflow vignette?

• Request that a new directory be created in our SVN repository under “/trunk/madman/workflows” and that you be given read/write access to this directory. You can request this access by emailing “maintainer at bioconductor dot org”. (You can view existing workflow sources here, username and password is readonly.)

• Write a vignette in LaTeX or Markdown, using the knitr package. Commit it to the svn location above. Alternatively, you can write a full R package in this location (in this case, it’s not required to use knitr for your vignette).

• The workflow builder will now try and build your vignette on Mac, Windows, and Linux. You’ll receive an email if there were any errors. You can monitor the progress of builds here.

• Every time you commit a change to your workflow directory, another build will be triggered and you will receive email if it fails.

• When you are ready for your workflow to appear on the Bioconductor web site, contact “maintainer at bioconductor dot org” and we will allow the workflow to propagate to our web site where it will be listed alongside the other workflows. It will be updated every time there is an SVN commit and a successful build.

## Using Math Symbols in a Markdown workflow vignette

If you want to include math symbols in a workflow vignette, put the following snippet at the beginning of your .Rmd file:

<script type="text/javascript"
src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
</script>


Then you can use math the same way you would in LaTeX, except the symbols for escaping it are different. For inline formulae, use \$$N\$$, and for displayed equations, use $$N$$.

The first will render as $$N$$ and the second as $N$.

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