Launching workflows
Workflows consist of sets of connected tools, with outputs from one analysis stage being used as input to later stages. Workflows are easily created using the graphical workflow editor in a CLC Workbench, and once installed on a CLC Server, they can be launched using a single command. Template workflows for many common analysis pipelines are delivered with the CLC Genomics Workbench and with several of its plugins and modules. Copies of template workflows can be installed on the CLC Server, like any other workflow.
By default, workflows installed on the CLC Server can be executed by all users, but access to each workflow can be controlled by the administrator.
The sections in this chapter focus on launching workflows using the command line:
- General information about launching workflows: General workflow launching information
- Providing input data: Specifying workflow inputs
- Saving outputs and exporting results: Specifying workflow outputs and exports
- Launching workflows containing Iterate elements: Launching workflows with Iterate elements
For general information about workflows, including creating them and configuring default settings, see the CLC Genomics Workbench manual.
For information on installing and configuring workflows on a CLC Server, see the CLC Genomics Server manual.
Subsections
- General workflow launching information
- Providing input data for analyses on a CLC Server
- Saving workflow outputs and exporting results
- Launching workflows with Iterate elements
- Launching workflows with Fork elements