[Bioc-devel] Workflow Package Updates / Guidelines
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
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
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