cwltool

cwltool is a command-line interpreter for the Common Workflow Language (CWL). CWL is a standard for describing computational workflows and tools, aiming to make them portable and reproducible across different environments. cwltool allows users to execute CWL workflows defined in YAML or JSON formats. It supports the execution of CWL versions 1.0, 1.1, and 1.2.

The primary function of cwltool is to take a CWL workflow or tool definition and the necessary input data, then execute the specified computational steps. It handles the complexities of parameter binding, file staging, and job execution, abstracting away the underlying infrastructure. This means a workflow defined with CWL can be run on a local machine, a high-performance computing cluster, or in cloud environments without modification to the workflow definition itself, provided the environment has cwltool and the necessary dependencies installed.

cwltool can execute workflows directly or generate scripts for other job execution engines, such as those used in HPC environments. It also provides features for debugging workflows and inspecting intermediate files. The tool is a key component for enabling reproducible and portable computational pipelines in scientific research and data analysis.