Reference Data

Reference Data are reference genome sets which you use to help look for deviations and to compare your data against.

Creating Reference Data

Reference data properties are located at the main navigation level and consist of the following free text fields.

• Types

• Species

• Reference Sets

Once these are configured,

1. Go to your data in Projects > your_project > Data.

2. Select the data you want to use as reference data and Manage > Use as reference data.

3. Fill out the configuration screen

You can see the result at the main navigation level > Reference Data (outside of projects) or in Projects > your_project > Flow > Reference Data.

Linking Reference Data to your Project

To use a reference set from within a project, you have first to add it. Select Projects > your_project > Flow > Reference Data > Link. Then select a reference set to add to your project.

Reference sets are only supported in Graphical CWL pipelines.

Copying Reference Data to other Regions

1. Navigate to Reference Data (Not from within a project, but outside of project context, so at the main navigation level).

2. Select the data set(s) you wish to add to another region and select Copy to another project.

3. Select a project located in the region where you want to add your reference data.

4. You can check in which region(s) Reference data is present by opening the Reference set and viewing Copy Details.

5. Allow a few minutes for new copies to become available before use.

You only need one copy of each reference data set per region. Adding Reference Data sets to additional projects set in the same region does not result in extra copies, but creates links instead. This is done from inside the project at Projects > <your_project> > Flow > Reference Data > Manage > Add to project.

Creating a Pipeline with Reference Data

To create a pipeline with a reference data, use the CWL - graphical mode. Projects > your_project > Flow > Pipelines > +Create > CWL Graphical. 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.

Safari is not supported for graphical CWL data.

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. After clicking the magnifying glass icon the user can select from provided options.