COSMOS: Python library for massively parallel workflows.

Authors :: Gafni E
Luquette LJ
Lancaster AK
Hawkins JB
Jung JY
Souilmi Y
Wall DP
Tonellato PJ
Source :: Bioinformatics (Oxford, England) [Bioinformatics] 2014 Oct 15; Vol. 30 (20), pp. 2956-8. Date of Electronic Publication: 2014 Jun 30.
Publication Year :: 2014
Abstract: Summary: Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services.<br />Availability and Implementation: Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://wall-lab.stanford.edu.<br />Contact: dpwall@stanford.edu or peter&#95;tonellato@hms.harvard.edu.<br />Supplementary Information: Supplementary data are available at Bioinformatics online.<br /> (© The Author 2014. Published by Oxford University Press.)