Script of Scripts: A pragmatic workflow system for daily computational research

PLoS Computational Biology
Gao Wang, Bo Peng

Abstract

Computationally intensive disciplines such as computational biology often require use of a variety of tools implemented in different scripting languages and analysis of large data sets using high-performance computing systems. Although scientific workflow systems can powerfully organize and execute large-scale data-analysis processes, creating and maintaining such workflows usually comes with nontrivial learning curves and engineering overhead, making them cumbersome to use for everyday data exploration and prototyping. To bridge the gap between interactive analysis and workflow systems, we developed Script of Scripts (SoS), an interactive data-analysis platform and workflow system with a strong emphasis on readability, practicality, and reproducibility in daily computational research. For exploratory analysis, SoS has a multilanguage scripting format that centralizes otherwise-scattered scripts and creates dynamic reports for publication and sharing. As a workflow engine, SoS provides an intuitive syntax for creating workflows in process-oriented, outcome-oriented, and mixed styles, as well as a unified interface for executing and managing tasks on a variety of computing platforms with automatic synchronization of files among ...Continue Reading

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Citations

Nov 25, 2020·Bioinformatics·Anthony WestbrookW Kelley Thomas
Jun 26, 2021·Computer Methods and Programs in Biomedicine·Gernot PlankEdward J Vigmond

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Methods Mentioned

BETA
RNA-seq

Software Mentioned

Rscript
Jupyter
CRAN
jupyterlab
samtools
Bpipe
NoWorkflow
Nextflow
R
pandoc

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