[Bioc-devel] Pipeline management (and AnnotationData Packages version)

Elena Grassi grassi.e at gmail.com
Wed Jun 22 08:42:02 CEST 2016

> We have been using snakemake (python-based, but essentially a domain language) with some pretty nice results.  Nextflow (groovy-based) and Toil are another couple that I am watching closely.  The Broad just released WDL and associated executors.  And common-workflow-language (CWL) is gaining traction as a way to write reproducible, sharable workflows.  None of these is directly R-based, but each will run any command-line software in a reproducible, scalable way.  The python-based workflow tools (Toil and snakemake) can directly execute R code using rpy2 integration if that is something you desire.

Thanks, I knew snakemake and nextflow but not the others and the
useful github collection.
Our internal system is http://bioinfotree.org/wiki/Main_Page (but the
website maintainer is not working here anymore therefore I do not know
how much of that is mantained :)) - I will look into integrating it
with docker and bioc annotation packages to see if something
interesting/useful comes out.

$ pom

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