The way the CLC Genomics Workbench checks whether a workflow already exists in a previous version is by looking at the workflow id. The id is a combination of the organization name and the name of the workflow itself as it is shown in the dialog shown in figure 9.12. Once installed this information is also available in the workflow manager (in figure 9.13 this is
CLC bio.Simple variant detection and annotation-1.2).
If you create two different workflows with the same name and using the same organization name when creating the installer, they cannot both be installed.
When new versions of the CLC Genomics Workbench are released, some of the tools that are part of a workflow may change. When this happens, the workflow may no longer be valid. This will happen both to the workflow configurations saved in the Navigation Area and the installed workflows. For the workflow configuration, you have to remove the invalid element and add the tool again. For installed workflows, there is no way to recover except asking the author of the workflow to update it and create a new version. We are working on improving this so that it becomes easier to recover when a new version is released.