[Bioc-devel] Workflow Package Updates / Guidelines

Shepherd, Lori Lori.Shepherd at RoswellPark.org
Fri Apr 13 19:16:56 CEST 2018

As mentioned before the workflows are in git and are now building on our
standard build machines.

The build reports are generated mon, wed, fri and can be seen here

Moving forward we want to align how we treat workflows with how we treat the
software and data experiment packages.

Some of this can already be seen on the biocViews section of the website
You'll notice we started adding specific Workflow biocViews terms based on the
categories that were used on the http://bioconductor.org/help/workflows/ page.
We have updated the workflow packages to include appropriate biocViews from this
page as well. The updated biocViews are already updated in the Bioconductor
git.bioconductor.org repositories and should be reflected on the website after
monday's build of the workflows. If anyone thinks additional workflow views
would be helpful please email lori.shepherd at roswellpark.org or post for
discussion on our community workflow slack feed

 Eventually, the http://bioconductor.org/help/workflows/ will be retired, as the
 workflows now have a standard landing page (linked off the biocViews page
 above). We will be adding redirects internally to hopefully protect any
 existing links in papers and such.

 Moving forward we will have a few additional requires for the  vignettes of
 workflow packages.  Namely that the  vignette has a meaningful name  and that
 it uses BiocStyle for formatting. This is an effort to standardize the
 workflows. Currently we will enforce  BiocStyle::html_document.  We are in  the
 works of developing a html_workflow_template. We encourage any vignettes that
 are not using this BiocStyle format to update the workflow vignette as soon as
 possible - eventually this update will be required.

Keep in mind also - that a proper version bump will be needed to trigger build
and propagation of workflows. And since the workflows will be building on
release and devel they should follow the similar guidelines regarding versioning

We welcome any feedback


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

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