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Reference Data

To use a reference set from within a project, you have first to add it. From the project's page select Reference Data > Manage > +Add to project. Then select a reference set to add to your project. You can select the entire reference set, or click the arrow next to it to expand it. After expanding, scroll to the right, to see the individual reference files in the set. You can select individual reference files to add to your project, by checking the boxes next to them.
To create a pipeline with a reference data use the CWL - graphical mode (important restriction: as of now you cannot use reference data for pipelines created in advanced mode). Use the reference data icon instead of regular input icon. On the right hand side use the Reference files submenu to specify the name, the format, and the filters. You can specify the options for an end-user to choose from and a default selection. You can select more than 1 file, but you can only select 1 at a time (so, repeat process to select multiple reference files). If you only select 1 reference file, that file will be the only one users can use with your pipeline. In the screenshot a reference data with two options is presented.
Two options for a reference file
If your pipeline was built to give users the option of choosing among multiple input reference files, they will see the option to select among the reference files you configured, under Settings.
Required settings
After clicking the magnifying glass icon the user can select from provided options.
Selections from the options