Feburary 05, 2020

Liz Kiernan
  • Updated

The following release notes correspond to January 20, 2020-February 05, 2020. This release includes back-end updates to Google Integrations and Notebooks to improve upcoming features.

Workflows

  • Terra now supports Dockstore WDL workflows that use relative imports from GitHub in addition to imports using the full-length URL.

What is a relative import?

When a workflow imports a file using the "import" command, it can specify that file's location by using an absolute path (a full length URL) or a path relative to the workflow's location (a relative import). WDL workflows often live in GitHub repositories and will import files from different folders within those repositories. Previously, Terra would only accept Dockstore workflows if they imported files using the full GitHub URL (as shown for the file "my_tasks.wdl" below). 

import "https://raw.githubusercontent.com/org/repo/dependencies/my_tasks.wdl"

Now, Terra supports Dockstore workflows that import files using a relative path in which only the repository folder needs to be specified (see how the code changes below for the "my_tasks.wdl" file).

import "dependencies/my_tasks.wdl"

 

Important Note: Dockstore currently disables the "Launch with Terra" button for WDLs with relative imports because Terra's support is brand-new. Users can work around this by navigating directly to the Import Workflow screen in Terra, located at https://app.terra.bio/#import-workflow/dockstore/{path}/{version}. 

You will have to manually enter the path and version of your workflow into the URL. In the example below, we have modified the Terra Import Workflow URL "https://app.terra.bio/#import-workflow/dockstore/{path}/{version}" to include the path for the Optimus workflow ("https://app.terra.bio/#import-workflow/dockstore/github.com/HumanCellAtlas/skylab/Optimus:optimus_1.3.6_terra_patch2"). 

Screen_Shot_2020-02-06_at_10.07.08_AM.png

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