Release Notes: October 2017

Posted by KateN on 3 Oct 2017 (4)

October 20, 2017

New Features

  • Users can now specify a snapshot comment when creating or editing a method in the Method Repository. The comment appears in the method config tab of a workspace, when importing/exporting methods, and when viewing a method in the Repository.


  • Now we explicitly state in the user interface that group functionality cannot be used in the Methods Repository. We are working on supporting this.

Bug Fixes

  • Two-dimensional Array entity attributes (e.g. [[1,2,3],[4,5,6],[7,8,9]]) can now be bound to two-dimensional array WDL inputs (e.g. Array[Array[Int]]).
  • Fixed an issue where after updating the owners of a method or method configuration inside the Method Repository, the new list of owners was not displayed until the page was refreshed.

October 17, 2017

New Features

A new UI for the Methods Repository has been released!

  • The Methods Repository page now only lists methods. Configurations based on those methods are now accessible via the Method's detail view.

  • The Methods detail view shows all snapshots at once - use the dropdown to switch between snapshots and compare them.

  • Export an existing Configuration to a workspace, or use a blank configuration.
  • You will be able to export any configurations that are compatible (i.e. have the same inputs and outputs) with the method snapshot of interest, even if the configuration was originally created based on a different method snapshot.


  • A Method Configuration in a workspace will now only let you set the root entity type to a type that exists in your workspace.
  • If you are in the filter box for a table and have entered text to search on, hitting escape will clear the search rather than closing the dialog as it did previously.
  • When you redact a snapshot of a method from the Methods Repository, you will now be warned that you will also remove all associated configurations from the repository.
  • The GA4GH's DUO ontology has now been integrated into the Library.

Bug Fixes

  • Fixed a bug where attempting to delete workspace attributes would occasionally delete the wrong row.
  • Fixed a bug where editing a workspace method configuration to point to a different method snapshot could cause the configuration to be unusable.
  • Using escape key to close the export method config modal was throwing a javascript error; this is now fixed.

October 3, 2017

New Features

  • A new level of Workspace permission has been added: Can Compute. This permission allows more granularity in sharing of the workspace. Without the can compute permission, a user can read and contribute to a workspace, but cannot launch an analysis.
  • We have a new category in our FireCloud API termed GA4GH Tool Registry that now includes a GET API which returns the WDL descriptor for the specified public method and is compatible with the GA4GH Tool Discovery API specs.
  • A new Methods Repository API endpoint returns all configurations in the repo that are associated with a specified method and compatible with a supplied method snapshot. Here, compatible means having the exact same set of input and output keys.


  • When exporting a method to workspace, the workspaces listed are filtered such that only those you have WRITE permissions or greater are listed.
  • You can now leave the Output Expression blank in the Method Configuration.
  • "TCGA Protected Access" has been renamed to "TCGA Controlled Access" in the search dropdown for workspaces.

Bug Fixes

  • Method Configurations with invalid inputs and/or outputs can no longer launch an analysis; These runs would fail shortly after launching, so we now stop them from launching.
  • The search checkbox for TCGA Open Access workspaces now functions as expected.
  • When re-uploading an edited WDL file to the Create a New Method dialog, it would show the original content rather than the updated file content. This has been fixed so it now displays the updated file content.
  • Fixed a regression in which the "Redact Snapshot XX" checkbox did not actually redact anything while editing a method in the Methods Repository.

Return to top

Tue 3 Oct 2017

dheiman on 3 Oct 2017

> @KateN said: > > #### Bug Fixes > - Method Configurations with invalid inputs and/or outputs can no longer launch an analysis; These runs would fail shortly after launching, so we now stop them from launching. Are these evaluated against the entity the config is being launched on? If so that is awesome! If y'all could expose such functionality via API, that would be amazing, as the [existing validate API](!/Method_Configurations/validate_method_configuration "existing validate API") only states if values aren't populated (wrongly reporting unpopulated optional inputs as invalid), and doesn't evaluate against an existing entity.

KateN on 3 Oct 2017

Apologies for the delay @dheiman; I did not see your message until today. Let me check with a developer and get back to you.

KateN on 3 Oct 2017

After speaking with a developer, I can tell you that yes, they are being evaluated against the entity the config is being launched on. If you try to launch on a non-existent attribute, you will be unable to launch the submission. I will put in a ticket to expose that via the API, as you've requested. However, wrongly reporting unpopulated option inputs as invalid in the API is definitely a bug, for which I will file a separate ticket. Thank you for your input!

breardon on 3 Oct 2017

I think that a bug may have been introduced in the release this morning (October 16th). It seems that http API requests are taking on the order of ~ 60 seconds, while https requests are still just as fast. These requests were made not on the Broad network. t = time.time() print requests.get("") elapsed = time.time() - t print 'time for HTTP request:', elapsed t = time.time() print requests.get("") elapsed = time.time() - t print 'time for HTTPS request:', elapsed returns the following: time for HTTP request: 59.2582259178 time for HTTPS request: 0.139764070511 After signing onto the Broad VPN, the HTTP request time is reduced to approximately 1 second, but it is still an order of magnitude longer than the HTTPS request time for HTTP request: 1.16983008385 time for HTTPS request: 0.151965141296

- Recent posts

- Follow us on Twitter



Check out the $5 genome analysis pipeline in our latest featured workspace:
22 Feb 18
@jasongallant Thank you, Jason, for such a kind compliment. We appreciate the feedback and are happy that you enjoy the product!
22 Feb 18
We've updated the preprocessing #GATK4, somatic CNV & SNV featured workspaces w/ time & cost benchmarks! Grab free…
17 Jan 18
#GATK4 Facebook live event will be on soon! Tune in 2 - 4 PM EST.
9 Jan 18
RT @broadinstitute: TOMORROW (1/9)! 2pm EST: #GATK4 Launch live on Learn about the new release's features & capabi…
8 Jan 18

- Our favorite tweets from others

@gatk_dev @BroadFireCloud @github We've been hacking GATK for years to play well with fish and butterflies! My enth…
23 Feb 18
@BroadFireCloud also does call caching!!!!!! Perfect for tinkering with multi-step pipelines.
23 Feb 18
Longtime GATK user, first time @BroadFireCloud user. #GATK4 is awesome, and Firecloud is like a dream. Seriously…
22 Feb 18
dedicating my #GalentinesDay to my gal of the moment, the broad's gatk website 💖💖💖💖
13 Feb 18
The @broadinstitute this week released #GATK4, the much-anticipated version 4 update to the Genome Analysis Toolkit…
10 Jan 18

See more of our favorite tweets...