Handling the output of an external tool
When Output file from CL is chosen for a parameter in the General configuration area, a drop down list appears beside it. The possibilities, and how those are configured, are:
- Do nothing with the output of the external command. Choose the option "No standard import or map to high throughput sequencing importer". Then do no further configuration of this parameter.
- Use a standard importer to import the results into the CLC Server. Select the relevant importer from the list displayed.
- Link the output to a high throughput sequencing importer or a tool on the CLC Server that should post-process the results. Choose the option "No standard import or map to high throughput sequencing importer" and then configure the relevant high throughput sequencing or post processing tool as described in High throughput sequencing importers and post processing tools
The empty text field beside the drop down list allows a default name to be configured for the data elements that are imported into the CLC Server. If this field is left blank and a standard importer has been selected, the base name of the file on the system is used as the base name for the resulting data elements in the CLC Server.
When Output file from CL is chosen for at least one parameter, the end user will need to provide a location on the CLC Server to store the results. This will be the case even if the output of the external file will not be imported, as log files will still be written to the location selected.