Authoring Bioconductor workflows with BiocWorkflowTools

Implementation

Given the intention for workflow documents to be full of executable examples that can be regularly checked and updated as necessary, it seems natural to recommend working with one of the literate programming formats available in R, rather than using a static typesetting tool. As previously mentioned, there are two formats commonly used here: Sweave and R Markdown. This immediately presents an author with a choice, even before a single word has been written, and there are reasonable arguments for electing to choose either; R Markdown has a simpler syntax and can be easily transformed into HTML for display on a website, while Sweave offers more precise control over document formatting and can readily be converted into a L^AT_EX format suitable for journal submission.

In order to streamline this, we have chosen to support only R Markdown as an input format, since this can be directly submitted to Bioconductor, with the conversion into the HTML format displayed on the website handled on their side. This then leaves the challenge of converting R Markdown into a format suitable for journal submission. To tackle this we have developed BiocWorkflowTools, an R package that provides article templates, conversion tools and the ability to upload documents to Overleaf.com (F1000Research’s preferred L^AT_EX submission system).

Operation

In order to use BiocWorkflowTools the user must already have R version 3.4.0 or newer installed on their system. We also recommend working in the RStudio environment, however this is optional and all operations can be carried out at the command line with instructions for both approaches provided below.

Installation

BiocWorkflowTools can be obtained from the Bioconductor package repository by running the following commands in your R session.

source("http://www.bioconductor.org/biocLite.R")
biocLite("BiocWorkflowTools")

Creating a Bioconductor workflow package

Given BiocWorkflowTools’s raison d’être is to ease the burden of meeting the distinct requirements of two publishing platforms in a hassle-free manner as possible, our recommended strategy assumes that most authors begin a project with the intention of submitting the final outcome to both Bioconductor and F1000Research.

For F1000Research, the list of material required is straight-forward and familiar: the article itself, a list of references, figures, and supplementary materials. These can then be sent as a collection of files. When it comes to Bioconductor all the same materials are required; however their computing infrastructure, which enables the regular document checking and easy distribution, also requires that the submission is made in the form of an R package. There are numerous resources discussing how to create an R package⁴ (and we would highly recommend potential authors to read these if they are not familiar with writing packages), but to streamline this process we provide the function createBiocWorkflow, which will create the minimum folder structure needed for submission to Bioconductor.

BiocWorkflowTools::createBiocWorkflow("MyWorkflow",
                                           quiet = TRUE,
                                           open = FALSE)

Running the example above will create a workflow package called MyWorkflow with the subdirectory vignettes containing an article template named MyWorkflow.Rmd. It is in this file that one should start developing their workflow document. In its initial state the template provides an exemplary skeleton of a typical workflow article, along with examples of how to include specific document features such as figures, tables, formulae and code blocks, in much the same way as the more traditional L^AT_EX and Microsoft Word templates available from F1000Research’s website. The template also includes an example of the required document header, where article metadata including the title, author names, their affiliations and the abstract are specified.

In the example above, changing the argument open = TRUE will open a new RStudio project rooted in the newly created MyWorkflow folder.

Writing only a workflow document

If you do not wish to make a complete package, and instead would simply rather use R Markdown to author an F1000Research article, the recommended platform for most authors is still to work in RStudio. Rather than creating a new package as before, the user can opt to create a new R Markdown document from the file menu and, assuming the BiocWorkflowTools package has been installed, will be presented with the option to use the F1000Research Article template (Figure 1).

Figure 1. Creation of a new article is integrated into RStudio.

The F1000Research template can be accessed via the ‘New R Markdown’ file menu dialog.

This will automatically open a new document based the F1000Research template described previously.

Working outside RStudio Even if you choose not to work in the RStudio environment, you can still use the included template to create a new file. We recommend using the template as a starting point to facilitate adherence to the required article structure. The command below will create a folder named MyArticle within the current working directory, and this in turn will contain the template MyArticle.Rmd which one can edit with the tool of choice.

rmd_file <- rmarkdown::draft("MyArticle.Rmd",
                                 template = "f1000_article",
                                 package = "BiocWorkflowTools",
                                 edit = FALSE)

Conversion to L^AT_EX

If you are using RStudio to edit your workflow, the simplest way to create the L^AT_EX version of your document is to press the ‘Knit’ button above the document pane in your workspace. This will process the document and generate both the L^AT_EX version and a compiled PDF so you can see how the final print version will look. This process also carries out some necessary housekeeping, such as copying the required F1000Research L^AT_EX style file and the journal logo into the same location as your document, so you may notice some additional files appearing.

If one prefers to work in an editor other than RStudio, it is still possible to transform the R Markdown file into L^AT_EX (along with the aforementioned housekeeping) by using the function render from the rmarkdown package. This will carry out much the same conversion process as using RStudio, executing the code chunks and producing the expected L^AT_EX and PDF output files.

rmarkdown::render(rmd_file)

Article submission

Ideally submission of a workflow is to both Bioconductor and F1000Research. Instructions for contributing to Bioconductor are available from https://www.bioconductor.org/developers/how-to/workflows.

Submission of L^AT_EX articles to F1000Research is currently performed using Overleaf.com, an online collaborative writing and publishing tool. Complete details are available online, but assuming one has already written an R Markdown workflow and generated a L^AT_EX source file, they can choose to upload the file directly to Overleaf using their web browser.

BiocWorkflowTools provides the function uploadToOverleaf as an alternative option for getting the article into the Overleaf system. This function takes the document directory and sends this to Overleaf, creating a new project for you automatically. The function will directly open the new project in a web browser.

BiocWorkflowTools::uploadToOverleaf("MyArticle")

BiocWorkflowTools::uploadToOverleaf("MyArticle")

At this point it is important to point out that both the L^AT_EX and R Markdown versions of the article are present in the Overleaf project, with the first of these being rendered into the document preview one sees on the site. In the Overleaf environment, only changes to the L^AT_EX version will be reflected in the preview pane, rather than the R Markdown the author has been working with until now. Thus it is easy for the two documents to become out of sync if edits are made using the browser interface. For this reason we recommend only working with Overleaf for the final submission process, and eschewing its document editing features at this point. Overleaf offers many attractive features such as collaborative editing between authors (particularly those who may not be familiar with the Rstudio environment) and live rendering of changes. However it should be emphasised again that it is natural to want to edit the L^AT_EX document in the Overleaf environment, which undermines the primary motivation behind BiocWorkflowTools, and as such our recommendation is to work exclusively on the Rmarkdown version of the article (using whichever version control system and collaborative tools the authors prefer) and then use Overleaf purely as a submission tool.

Article revisions

Assuming the article is provisionally accepted, the journal editors will create a second, private, Overleaf repository for minor copy editing. Editorial comments and instructions will be included in the R Markdown document, enclosed in comment tags e.g. <!-- Editorial comment -->.

At this stage one can make changes to the R Markdown document in the web browser interface, however there is currently no way to regenerate the L^AT_EX containg the changes from here. Instead, to make additional changes after an Overleaf project has been created, we recommend utilising the fact that all Overleaf projects can be interfaced using git. Instructions for initialising this on your local machine provided by Overleaf⁵. Since this is a private project the author will need to supply their Overleaf username and password to use git. If the manuscript is already under git version control, the Overleaf server can be added as an additional remote repository. Authors can then work on the manuscript offline, and use the regular git commands to keep the local copy in sync, such as git pull to get the latest version from Overleaf. Before committing any edits made to the source Rmd file remember to also regenerate the L^AT_EX output file. Once they are ready to push the changes back to Overleaf, they will instantly appear online.

cd MyArticle
git pull
# make some changes and regenerate the Latex file
git commit -a -m "My edits"
git push

Once the author is happy they have addressed the editor’s comments resubmission can be performed via Overleaf.