SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines | Zendy

Samuel Lampa | Zendy; Martin Dahlö | Zendy; Jonathan Alvarsson | Zendy; Ola Spjuth | Zendy

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SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines

Author(s) -

Samuel Lampa,

Martin Dahlö,

Jonathan Alvarsson,

Ola Spjuth

Publication year - 2019

Publication title -

gigascience

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 2.947

H-Index - 54

ISSN - 2047-217X

DOI - 10.1093/gigascience/giz044

Subject(s) - workflow , computer science , workflow management system , workflow technology , scripting language , software engineering , agile software development , perl , pipeline transport , python (programming language) , workflow engine , automation , programming language , database , engineering , environmental engineering , mechanical engineering

The complex nature of biological data has driven the development of specialized software tools. Scientific workflow management systems simplify the assembly of such tools into pipelines, assist with job automation, and aid reproducibility of analyses. Many contemporary workflow tools are specialized or not designed for highly complex workflows, such as with nested loops, dynamic scheduling, and parametrization, which is common in, e.g., machine learning.

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