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 described below.
In the last field presented, the name of the file the external process is expected to produce can be entered. If this field is left blank, the base name of the file produced by the external tool will be used as the base name for the data element imported into the CLC Server.
- 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.
- 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
- Use a standard importer to import the results into the CLC Server. Select the relevant importer from the list displayed. Specifying a default filename, including the relevant suffix (e.g. .fasta, .xlsx), in the final field is recommended.
If the import type Automatic is selected, the importer used is determined by the filename suffix in combination with a check of the format of the elements in the file. If the file type is not recognized, it will be imported as an external file. A list of file formats, including the expected filename suffix for each format, can be found in the appendix of the CLC Genomics Workbench manual: Read more about search here: http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Local_search.html.
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.