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• Introduction
• Installation
• Basic usage
• Handling passwords
• Managing SSL certificates
• Specifying locations of inputs, outputs and exports
  • Getting the ID form of a CLC URL
• Result files and connecting analyses in pipelines
• Launching workflows
  • 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
• Emptying the recycling bin for a CLC Server File Location

Launching workflows with Fork elements

When a workflow contains a Fork () element, the downstream path from that element must be specified when launching the workflow.

Fork elements are described in detail at: https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Fork.html.

As standard, running an incomplete command will result in information about missing parameters being listed. The names and values for parameters associated with Fork elements are defined by the workflow author. Specifically:

• The name assigned to the Fork element is used as the basis of the parameter name.

• Path names specified in the Fork element are the valid values for the parameter.

Figure 8.4 shows a workflow containing two Fork elements. The command for launching this workflow includes the following parameters:

• --map-dna-reads-to-reference Used to specify whether or not to analyze DNA reads using Map Reads to Reference. The valid values for this parameter are Yes and No.
• --run-rna-seq-analysis Used to specify whether or not to run analyze RNA reads using RNA-Seq Analysis. The valid values for this parameter are Yes and No.

The workflow author can optionally define a default value for each Fork element, in which case, that parameter is not required in the command.

Figure 8.1: Two Fork elements (dark green) have been renamed to indicate the choices available when the workflow is run. Where Yes is specified as the value, the analyses connected downstream of the Yes output channel are run.

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