dnanexus/dxCompiler 2.10.1

dxCompiler 2.10.1

on GitHub

• WDL: Fragments and blocks reuse applets as well, i.e. they are not rebuilt if the code corresponding to them hasn't been updated in the WDL source file. Previously only tasks were reused. Breaking: can break the logic of any App reuse for CWL (even tasks maybe are not reused), because ApplicationCompiler and WorkflowCompiler now look at the DocContents for checksum, and SourceCode attribute is now ignored.
• CWL: NetworkAccess, WorkReuse and ToolTimeLimit hints are now supported
• WDL: Update custom reorg applet (used for custom handling of your workflow outputs) example in documentation.
• WDL: Fix to the order of precedence for the different job reuse settings. The ignoreReuse setting specified in the extras.json file should override the dx_ignore_reuse setting specified in the runtime section of the WDL file.
• Updates to the documentation, esp. sections about delay workspace destruction, DNAnexus-specific runtime settings, and outputing DNAnexus files.
• WDL: Fix to configuring network access to tasks (applets). Now you can disable network access to your tasks with the runSpec.access setting in the extras.json file:

{
  "defaultTaskDxAttributes" : {
    "runSpec": {
        "access" : {
          "network": []
        }
      }
  }
}

However, if the task needs network access since it uses a Docker image from an external registry (e.g. DockerHub), the setting will be overwritten and full network access will be given to the task. You can prevent this by storing the Docker image as a file in your DNAnexus project.

Note that the setting above is under defaultTaskDxAttributes, which means it will be the default setting for all tasks; follow these instructions to configure a specific task.

Dependency updates

cwlScala 0.8.1

• Fixes CWL default requirement classnames NetworkAccess, WorkReuse and ToolTimeLimit so the corresponding hints can be recognized by dxCompiler (instead of being defined as GenericHints which are not interpreted during compilation).

wdlTools 0.17.9

• TAT.Workflow has a source attribute in analogy to TAT.Document to be used for checksum calculation for App/Job reuse
• Fixes evaluation of structs as input parameters of workflow/scatter: hash inputs are coerced from object to struct, and their optional elements are assigned to Null if not specified in job inputs.