broadinstitute/cromwell 54

on GitHub

54 Release Notes

Bug Fixes

• Fixed a bug where write_json() failed for Array[_] inputs. It should now work for Boolean, String, Integer, Float,
  Pair[_, _], Object, Map[_, _] and Array[_] (including array of objects) type inputs. More information on WDL Type to JSON Type
  conversion can be found here.

Spark backend support removal

Spark backend was not widely used and it was decided to remove it from the codebase in order to 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.

Per-backend hog factors

Cromwell now allows overriding system-level log factors on back-end level. First, Cromwell will try to use hog-factor
defined in the backend config, and if it is not defined, it will default to using system-wide hog factor.

backend {
  providers {
    PAPIv2 {
      config {
        hog-factor: 2
      }
    }
  }
}

For more information about hog factors please see this page.

martha_v2 Support Removed

Cromwell now only supports resolving DOS or DRS URIs through Martha's most
recent metadata endpoint martha_v3, dropping support for Martha's previous metadata endpoint martha_v2. To switch to
the new version of Martha's metadata endpoint, update the martha.url found in the filesystems
config to point to /martha_v3. More
information on Martha's martha_v3 request and response schema can be found
here.

DOS/DRS localization_optional Support

When running on a backend that supports localization_optional: true any DOS or DRS File values in the generated
command line will be substituted with the gsUri returned from Martha's martha_v3 endpoint. More information on
localization_optional can be found here.

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.