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. 2021 Nov 4;11:21680. doi: 10.1038/s41598-021-99288-8

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© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Bioinformatics workflows with multiple levels of complexity warrant a modular construction. It is easiest to program the workflow when its logic is abstracted away (in Tasks, red) from the command line invocations (in Bash scripts, pink) of the bioinformatics tools (light pink). Individual workflows can be further used as subworkflows of a larger Master workflow (e.g., Fig Supplementary 1). This architecture facilitates expression of additional complexity due to optional modules (dashed line), nested levels of parallelism (groups of arrows connecting red rectangles) and scatter-gather patterns (task 2 scattered across samples being merged into task 3).