dnanexus/dxCompiler 2.7.0

dxCompiler 2.7.0

on GitHub

• Handles empty scatters in WDL workflows
• Reserved parameters are now placed in the "Reserved for dxCompiler" parameter group (only affects the display of the app/workflow in the UI)
• Enables other metadata (title, description, version, etc.) to be set via extras.json
• When using manifests, passes any expression values from the helper applet to the called applet workflow so they are added to the output manifest
• When an applet calls executables, adds executables to bundledDepends to support cloning of workflows
• Executor creates hard- rather than soft-links in the input directory, so that linked files are accessible from within containers
• Fixes bug where default input values were not overridden for task inside subworkflow
• Adds support for specifying native app(let) in runtime section
• Fixes some type conversion bugs related to CWL Any type
• Affected by a bug for workflows that include a native platform app via dxni. Bug fixed in v2.8.1.
• Logs entire contents of WDL command at runtime

Warning: we discovered a regression in this release that may cause tasks to fail with out-of-disk errors due to excessive logging. Please update to 2.7.1 or later.

Dependency updates

dxApi 0.10.1

• Fixes resolveProject to handle container- objects
• Improves error message when API call fails due to connection error

cwlScala 0.7.1

• Handles error when listing folder during path value finalization

wdlTools 0.17.2

• Fixes infinite loop when calling wdlTools.eval.Runtime.contains with "docker" or "container"