COSMOS: Python library for massively parallel workflows.

Citation:

Gafni E, Luquette LJ, Lancaster AK, Hawkins JB, Jung J-Y, Souilmi Y, Wall DP, Tonellato PJ. COSMOS: Python library for massively parallel workflows. Bioinformatics. 2014;30 (20) :2956-8.

Date Published:

2014 Oct 15

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. 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. CONTACT: dpwall@stanford.edu or peter_tonellato@hms.harvard.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.