Selecting the root entity type

If you run a workflow from the Workflows page, you need to select the correct "root entity type" (i.e., input table) from the drop-down menu. This article gives guidance for determining the root entity type when you have several tables to choose from.   

Root entity type: Overview

The root entity type is the smallest piece of data a workflow can use as input. Selecting from the "root entity type" drop-down menu (Step 1 in the workflow configuration form) tells the workflow which table has the input metadata needed to run the workflow.

Note: Tables can be nested. For example, if your workflow runs on sets of data (arrays), the root entity type could be a sample_set or specimen_set table, even though links to the data files are ultimately in a sample or specimens table. 

Finding the root entity typeIf you can run your workflow on a single entity (like a specimen or  sample) 
The root entity type is that entity (i.e. specimen or sample)

If your workflow takes an array as input and cannot run on a single file
1. The root entity type could be a set table (i.e. sample_set or specimen_set).


2. The root entity type could be an entity table (i.e. sample) with an array of data files in one column.


If you run a somatic workflow (on tumor/normal pairs)
The root entity type is pair 

Root entity type examples

See the examples below for ways to determine the input entity type your WDL expects (could be a single entity table, a set table, or a pair table).

• If your workflow can run on a single entity, the root entity is a table of single entities (i.e., sample or specimen).

  How to verify

  Look in the Inputs tab of the workflow form. The Input Type is "File".
  

• If your workflow runs on an array of files, the root entity can be a set table (i.e., sample_set or specimen_set) or an entity table (i.e., sample or specimen) with an array in a column.

  How to verify

  Look in the Inputs tab of the workflow form. The Input Type is "Array[File]".
  

   

• If you run a somatic workflow, the root entity is pair. The file type could be File or Array[File] (depending on the workflow).