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COSMOS: Python library for massively parallel workflows.

Erik Gafni¹, Lovelace J Luquette¹, Alex K Lancaster²

¹Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP, Morocco.

Bioinformatics (Oxford, England)

|July 2, 2014

Summary

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This summary is machine-generated.

COSMOS is a Python library designed for efficient workflow management in next-generation sequencing pipelines. It streamlines the processing of clinical genomic data for translational research, offering job partitioning and progress tracking.

Area of Science:

Genomics
Bioinformatics
Translational Biomedical Science

Background:

Efficient workflows are crucial for processing clinical genomic data.
Next-generation sequencing (NGS) pipelines require robust management systems.

Purpose of the Study:

To introduce COSMOS, a Python library for workflow management.
To facilitate the handling of clinically generated genomic data in translational research.

Main Methods:

COSMOS provides formal description of pipelines and job partitioning.
It includes a user interface for job progress tracking.
The library abstracts queuing systems and offers fine-grained workflow control.

Main Results:

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COSMOS enables workflow creation on both traditional computing clusters and cloud services.

It simplifies the management of complex NGS pipelines.

Conclusions:

COSMOS enhances the efficiency of genomic data processing in translational science.
The library supports flexible deployment across diverse computational environments.