Introduction

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

Publications

  1. COSMOS: Python library for massively parallel workflows.
    Cite this
    Gafni E, Luquette LJ, Lancaster AK, Hawkins JB, Jung JY, Souilmi Y, Wall DP, Tonellato PJ, 2014-10-01 - Bioinformatics (Oxford, England)

Credits

  1. Erik Gafni
    Developer

    Center for Biomedical Informatics, Harvard Medical School, Morocco

  2. Lovelace J Luquette
    Developer

    Center for Biomedical Informatics, Harvard Medical School, Morocco

  3. Alex K Lancaster
    Developer

    Center for Biomedical Informatics, Harvard Medical School, Morocco

  4. Jared B Hawkins
    Developer

    Center for Biomedical Informatics, Harvard Medical School, Morocco

  5. Jae-Yoon Jung
    Developer

    Center for Biomedical Informatics, Harvard Medical School, Morocco

  6. Yassine Souilmi
    Developer

    Center for Biomedical Informatics, Harvard Medical School, Morocco

  7. Dennis P Wall
    Developer

    Center for Biomedical Informatics, Harvard Medical School, Morocco

  8. Peter J Tonellato
    Investigator

    Center for Biomedical Informatics, Harvard Medical School, Morocco

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Summary
AccessionBT006803
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionMorocco
Submitted ByPeter J Tonellato