RT Journal Article
SR Electronic
T1 Flowr: Robust and efficient pipelines using a simple language-agnostic approach
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 029710
DO 10.1101/029710
A1 Sahil Seth
A1 Samir Amin
A1 Xingzhi Song
A1 Xizeng Mao
A1 Huandong Sun
A1 Andrew Futreal
A1 Jianhua Zhang
YR 2015
UL http://biorxiv.org/content/early/2015/10/22/029710.abstract
AB Motivation Bioinformatics analyses have become increasingly intensive computing processes, with lowering costs and increasing numbers of samples. Each laboratory spends time creating and maintaining a set of pipelines, which may not be robust, scalable, or efficient. Further, the existence of different computing environments across institutions hinders both collabo-ration and the portability of analysis pipelines.Results Flowr is a robust and scalable framework for designing and deploying computing pipelines in an easy-to-use fashion. It implements a scatter-gather approach using computing clusters, simplifying the concept to the use of five simple terms (in submission and dependency types). Most importantly, it is flexible, such that customizing existing pipelines is easy, and since it works across several computing environments (LSF, SGE, Torque, and SLURM), it is portable.Availability http://docs.flowr.space