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- a lot of weird (but powerful) syntax (
) - a meager set of built-in data types
- functions and scripts can only return one small integer value
- the proxy for this is capturing output, but this can be tricky
- no support for object oriented programming
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These days, complex pipelines may be difficult to write in any single programming language; thus workflow managers are becoming increasingly popular. These tools allow the integrated orchestration of many different workflow components, potentially written in many different languages, managing their dependencies via rules (think make, on steroids), and can also be effectively deployed in cloud environments such as AWS and Google Cloud. Both Nextflow and Snakemake, two of the most popular workflow managers, support rule bodies written in bash (and in other languages).
Bash in the world
bash scripting is much in demand. And while it may not be loved by programmers, developers who know it are well compensated.
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