Workflow engine for large-scale sequence data


Alex was a member of the team that developed the open-source COSMOS: a Python library to manage large-scale scientific workflows that allows formal description of pipelines and partitioning of jobs developed for (but not restricted to) running next-generation sequencing (NGS) workflows. It includes a user-interface for tracking the progress of jobs, abstraction of the job queuing system (to allow interface to multiple queuing systems) and fine-grained control over the workflow. COSMOS runs on cloud-based services such as Amazon Web Services and Google Cloud, as well as traditional high-performance computing (HPC) clusters. COSMOS is available as open-source under the GNU GPL license: along with a genome analysis workflow, GenomeKey (released under the MIT license).

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