CLC Microbial Genomics Module offers several workflows. For a general introduction to workflows, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Workflows.html.
A workflow tutorial is available at http://www.http://resources.qiagenbioinformatics.com/tutorials/Workflow-intro.pdf.
Workflows can be used "as is", or can be customized for common use cases.
The following workflows can be run in batch. Running in batch allows you to select several items and create as many sets of output files as items you selected.
To explore the content and parameters of a template workflow, select the workflow, right click on its name and select the choose the option Open Copy of Workflow. You can pre-set and save parameters and input files directly from the copy of the workflow in the View Area, which is useful is you intend to run the exact same workflow repeatedly. Otherwise just double-click on the workflow's name in the Navigation Area and follow the instructions on each wizard step.
The following sections describe how to configure the provided 12 workflow templates that are recommended as the starting points for your metagenomics or typing- and epidemiological analyses. Relevant example data can be downloaded and imported by following the tutorial on OTU clustering using workflows (see https://resources.qiagenbioinformatics.com/tutorials/OTU_Clustering_Workflows.pdf) and Typing and Epidemiological Clustering of Common Pathogens (see http://resources.qiagenbioinformatics.com/tutorials/Typing_Epidemiological_Clustering.pdf).
Note! The typing and epidemiology template workflows automatically associate the analysis results to a Result Metadata Table specified by the user. Searching and quick filtering of the sample metadata and the generated analysis result data enable the selection of data subsets that can be in turn used for additional downstream SNP tree analyses.