dxCompiler 2.9.0

2.9.0 2022-02-08

• Command file is now echoed to stderr rather than stdout
• Fixes a bug where directory support was broken for WDL; directories in WDL are represented as strings
• Switches from using cwltool to cwlpack
• Fix an issue with default values in CWL
• Adds support for publishing global workflows from dxCompiler-generated WDL workflows; see documentation
• Fix an error message detecting unsupported CWL version
• Update sbt to 1.6.1

Dependency updates

cwlScala 0.8.0

• Breaking
  • Parser API has changed substantially, with parameters added, removed, and rearranged
  • Parser.parse method is now private - use parseString or parseFile instead
  • Removes all options to modify IDs during parsing
• Handles workflows packed by cwlpack
• Adds Process.simpleName method to return simplified process name from ID automatically generated by cwlpack --add-ids
• Adds Identifiable.copySimplifyIds method to deep-copy objects with simplified IDs
• Adds CwlEnum.symbolNames function for getting enum symbols without any namespace prefixes
• Adds coerce option to Evaluator.evaluate to actually perform type coercion, rather than just checking that the result is coercible to the specified type
• Trims StringValue when coercing to primitive types
• Fixes Evaluator.finalizeInputValue for compound and optional types
• Evaluator.finalizeInputValue loads file contents from remote file source if file does not exist locally
• CwlType.coerceTo now returns both the coerced-to type and value
• Added CwlType.CwlGenericRecord, which is coercible to either CwlInputRecord or CwlOutputRecord
• Fixes evaluation of values with multiple possible types