About Workflows / Meta-Tools

Workflow tools – or meta-tools – wrap several tools to form a unified pipeline. These workflow tools are usually focused specific area like microbiome or single-cell analysis, but they wrap more generic tools under the hood.

They're popular, because they're easy to use; there's no need to make your own choices on aligners, assemblers, or classifiers, and the tools the workflow creator chooses are often pre-tuned for one specific use-case.

HUMAnN is a perfect example of these types of meta-tools. Under the hood, it uses:

• Bowtie 2
• Diamond
• Python 3
• RAPSearch2
• MetaPhlAn 3

and several other tools, all wrapped under the humann command.

When using workflow tools via Toolchest, you'll notice a new argument: mode. This lets you run sub-tools directly.