The inputs and outputs are as configured in the external application itself. In figure 12.18, the external application, CLC bio Bowtie Map is used as a workflow element. In this particular case, the configuration had a single post processing step, the Import SAM/BAM Mapping Files tool. That tool can output a stand-alone read mapping or a read mapping track, and outputs a sequence list containing unmapped reads. Thus these are the output options you see in the workflow element.
Figure 12.18: The CLC bio Bowtie Map external application used as an element in a workflow. Here, the outputs visible are those provided by the (single) post processing tool configured: Import SAM/BAM Mapping Files
When additional post processing tools are configured, their outputs will be added to those available in the workflow element. See figure 12.19, where a workflow element for the external application, CLC bio Bowtie Map is present, but in this case, the configuration specified two post processing tools: the Import SAM/BAM Mapping Files tool and the Fasta High-Throughput Sequencing Import tool. As earlier, the three outputs associated with the Import SAM/BAM Mapping Files tool are present. In addition, the output from the Fasta High-Throughput Sequencing Import tool, "Imported reads" is present.
The output channel names make sense for individual tools, but may not make sense in the context of a given external application. For example "Imported Reads" makes sense when you run the Fasta High-Throughput Sequencing Import tool by itself. However, in the context of the CLC bio Bowtie Map external application, it is not indicative of what is really being output. Meaningful names can be set on the workflow output elements themselves though, providing more information to the workflow user about what a particular output is. See for example figure 12.19, where the output from the Fasta High-Throughput Sequencing Import tool, "Imported reads", has been renamed "bowtie multimapped reads".
Figure 12.19: The CLC bio Bowtie Map external application used as an element in a workflow. Here, the outputs visible are those provided by the post processing tools configured: Import SAM/BAM Mapping Files and Fasta High-Throughput Sequencing Import.
Limitation: External applications can only be used in a workflow if they are configured with at least one "User-selected input data" and at least one import of the data generated. If the external application does not generate data that is suitable for import then importing the output from standard out or standard error as plain text is recommended. In general it is recommended to always import standard error to help identify potential problems with an external application.
For more details about designing and running workflows, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Workflows.html.