• Added DIY Docker image instructions. This replaces the Docker image published to Docker Hub, which is now deprecated.
• Added exponential backoff and retry, including attempt to get password from AWS, in ECR docker script template

• Update dxda to 0.6.2 and dxfuse to 1.4.0

• Optimize with bulk file describe during scatter collect, also for files inside arrays and structs.

Dependency updates

dxApi 0.13.10

• Updated wdlTools and its dependencies
• Updated dxApi
• WDL workflows allow headJobOnDemand for the tasks if this spec is passed through extras via runSpec.headJobOnDemand.

Dependency updates

wdlTools 0.17.17

• ANTLR4 version bump to 4.13.1

cwlScala 0.8.5

• ANTLR4 version bump to 4.13.1

dxApi 0.13.9

• adds headJobOnDemand attribute to jobNew call

• changes to allow compiling with treeTurnaroundTimeThreshold attribute which facilitates platform to send the email
  notifications for the root jobs/analyses with a run time (aka treeTurnatoundTime) exceeding the specified threshold.
  The attribute treeTurnaroundTimeThreshold can be specified for tasks and workflows via extras.json. This feature is
  not exclusive for dxCompiler and more information is available in the platform documentation.

Dependency updates

dxApi 0.13.8

• WDL: eliminates inefficient file-XXX/describe API calls and replaces them with a bulk describe (i.e `system/findDataObjects)

Dependency updates

dxApi 0.13.6

dxFileAccessProtocols 0.5.6

• changes to facilitate the optimizations of number of file-xxx/describe API calls upon (de)localization of input/output files

• fixes awscli dependency
• dxda version update to v0.6.0 to address occasional filesystem errors seen in DNAnexus jobs.
• Fixes for the -pretty flag in the describe command.
• WDL: fix for the tasks wrapped in a frag with optional inputs. Those inputs get forcibly evaluated to explicit null
  and cause inconsistencies with applet inputs. This is fixed and all implicit null (None) values of optionals are remaining implicit.
• Updated dxfuse to v1.1.1

Dependency updates

wdlTools 0.17.16

• New value type V_ForcedNull is used to avoid an addition of an explicit null input to an Optional value. Previously,
  if a task was wrapped in a frag - in some cases Optionals without a value were forced to be an explicit null. This version
  fixes such behavior.
• Draft-2 parser. Previous behavior: if version is not declared, it is assumed to be draft-2, which has no formal
  input definitions for tasks and workflows. However, if a user forgets to declare the version while working on workflow
  of a version greater than draft-2 with formal definition of input, the parser fails to follow the syntax and throws
  the errors not related to the version or the formatting of the input section. Here this behavior is fixed: if version
  is not detected and draft-2 is assumed, we check if the input section is defined and throw an exception in this case.

• Option delayWorkspaceDestruction was deprecated and will be ignored when included in extras.json. To preserve the
  workspace, --delay-workspace-destruction flag should be included in dx run workflow-XXX.
• Minor fixes.

• dxda update to v0.5.12 which adds a retry for file download. This fixes the "context canceled" error which was
  thrown due to the dxda behavior.

Dependency updates

dxApi 0.13.5

• WDL: fixes a runtime error when a scatter over an empty array tries to return an empty array. Error occurred
  specifically when a task wrapped in a scatter fragment had an array among the outputs. Currently, evaluation of a task
  over an empty array returns an empty array, and the wrapped task is not executed.
• WDL: fixes a runtime error when a private variable is accessed by index then by key (e.g. my_var[0].left).
• Minor: error message now suggests to compile with -archive flag instead of the deprecated -a flag when an applet
  with duplicate name exists.
• Minor. WDL: removed obsolete warning messages when compiling with parameter_meta section in WDL source.

Dependency updates

dxApi 0.13.4

• Fixes handling of suggestions field for IO specs when only project ID is specified. Now instead of exception
  a warning is thrown.