Workflow Editor¶
Which workflow environment to choose for running OpenMS tools?
You can run OpenMS TOPP tools from the command line using your custom scripts, or use powerful workflow systems designed to make workflow creation and maintenance more fun:
Free, open source, desktop app. An analytics platform with workflow editor and a nice drag-and-drop user interface. Very interactive and has built-in nodes for related tasks like working with chemical structures, databases, machine learning, scripting. Distributed computing is best achieved with a KNIME server (License required) which also allows user management and a web interface to interact with workflows. In KNIME you can easily construct your own workflows or just download our ready-made creations for the most common analysis tasks.
Free, open source, desktop app. An analytics platform with workflow editor and a nice drag-and-drop user interface. Very interactive and has built-in nodes for related tasks like working with chemical structures, databases, machine learning, scripting. Distributed computing is best achieved with a KNIME server (License required) which also allows user management and a web interface to interact with workflows. In KNIME you can easily construct your own workflows or just download our ready-made creations for the most common analysis tasks.
Script/DSL-based workflow language, executor and utilities (such as the browser based launcher and supervisor nf-tower). Automatically runs on various different cloud (AWS, Google, …) and HPC environments (SLURM, LFS, Kubernetes, …). It is recommended to use our ready-made nf-core compatible workflows for ease of use via the browser-based configuration and launcher.
Script/DSL-based workflow language, executor and utilities (such as the browser based launcher and supervisor nf-tower). Automatically runs on various different cloud (AWS, Google, …) and HPC environments (SLURM, LFS, Kubernetes, …). It is recommended to use our ready-made nf-core compatible workflows for ease of use via the browser-based configuration and launcher.
Server and browser-based interactive workflow editor and runner. A public server instance can be used for testing and smaller experiments. Provides nice guided tutorials.
Server and browser-based interactive workflow editor and runner. A public server instance can be used for testing and smaller experiments. Provides nice guided tutorials.
OpenMS’ build-in workflow system, with limited capabilities but easy to use and tailored to TOPP tools.
OpenMS’ build-in workflow system, with limited capabilities but easy to use and tailored to TOPP tools.
OpenMS tools can self-generate CWL tool descriptions. As of OpenMS 3.6, TDL support is disabled by default; official binary releases include it. Rebuild with -DENABLE_TDL=ON to enable CWL generation.
OpenMS tools can self-generate CWL tool descriptions. As of OpenMS 3.6, TDL support is disabled by default; official binary releases include it. Rebuild with -DENABLE_TDL=ON to enable CWL generation.