High-throughput technologies, such as next-generation sequencing, have turned molecular biology into a\ndata-intensive discipline, requiring bioinformaticians to use high-performance computing resources and carry out\ndata management and analysis tasks on large scale. Workflow systems can be useful to simplify construction of\nanalysis pipelines that automate tasks, support reproducibility and provide measures for fault-tolerance. However,\nworkflow systems can incur significant development and administration overhead so bioinformatics pipelines are\noften still built without them. We present the experiences with workflows and workflow systems within the\nbioinformatics community participating in a series of hackathons and workshops of the EU COST action SeqAhead.\nThe organizations are working on similar problems, but we have addressed them with different strategies and\nsolutions. This fragmentation of efforts is inefficient and leads to redundant and incompatible solutions. Based on our\nexperiences we define a set of recommendations for future systems to enable efficient yet simple bioinformatics\nworkflow construction and execution.
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