November 19, 2020

Liz Kiernan
  • Updated

These release notes correspond to November 10, 2020 - November 19, 2020. This release includes back-end updates to Workflows and Google Integrations.

 

Notebooks

  • The Python package enum34 has been removed from the terra-jupyter-python image. The image now uses the standard library enum module by default.
  • The RStudio Terra image was updated with Bioconductor v3.12 and R v4.0.3. For a description of the Bioconductor changes, see https://bioconductor.org/news/bioc_3_12_release/.

User Interface

  • Cost estimates for Spark clusters using both workers and preemptibles were updated to be more accurate.
  • Fixed a bug that could cause a workflow imported from Dockstore to display an outdated version in the Terra if a floating reference is used (e.g. "dev" or "master"). Workflows stored in the Broad Methods Repository were not affected.

Workflows

  • Cromwell 54 has been released (see the official Release notes here). The following summarizes the updates:
    • Fixed the write_json() for Array[_] inputs. It should now work for Boolean, String, Integer, Float, Pair[_, _], Object, Map[_, _] and Array[_] (including array of objects) type inputs
    • Removed Spark backend support; it was not widely used and its removal helps narrow the scope of Cromwell code
    • Improved DRS Localizer logging. Error logging while localizing a DRS URI should now be more clear, especially when there is a Requester Pays bucket involved
    • Enabled overriding system-level hog factors on back-end level (more details here)
    • Removed martha_v2 support; only the most recent martha will be used. To switch to
      the new version of Martha's metadata endpoint, update the martha.url found in the filesystemsconfig to point to /martha_v3
    • Added DOS/DRS localization_optional support; more information can be found here.
    • Made DOS/DRS metadata retrieval retried by default. Attempts to retrieve DOS/DRS metadata from Martha will be retried by default. More information can be found here 
       

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