Ten simple rules and a template for creating workflows-as-applications.

There is a growing trend for releasing bioinformatics workflows as command line applications. This is a good thing as workflow management systems add both functionality and reliability, while command line interfaces are convenient for end users. Developing command line software in this way is considerably faster. However, there are many potential pitfalls that developers of bioinformatics tools should avoid. We outline ten simple rules for converting workflow manager pipelines into command line applications, and present working examples that also function as templates using the two most popular workflow managers, Snakemake (github.com/beardymcjohnface/Snaketool) and Nextflow (github.com/beardymcjohnface/Nektool).