Running the analysis and organizing the results

At the last dialog before clicking Finish, it is only possible to use the Save option. When a tool is run in batch mode, the default behavior is to place the result files in the same folder as the input files. In the example shown in figure 8.3, the result of the two single sequences will be placed in the Cloning folder, whereas the results for the Cloning vector library and Processed data runs will be placed inside these folders.

However, there is an option to save the results in a separate folder structure by checking Into separate folders. This will allow you to specify a new save destination, and the CLC Genomics Workbench will create a subfolder for each batch unit where the results are saved..

When the batch run is started, there will be one "master" process representing the overall batch job, and there will then be a separate process for each batch unit. The behavior of this is different between Workbench and Server:

If you need to stop the whole batch run, you need to stop the "master" process.