dnanexus/dxCompiler 2.10.2

dxCompiler 2.10.2

on GitHub

• WDL: Fix to native app(let)s instance override with system requirements (cpu/memory/disks) in case of the direct calls and executions within fragments. Only -instanceTypeSelection static (default) is supported. If compiled with dynamic - default instances will be used.
• CWL: Partial implementation of task/fragment applets and workflows reuse. Same as in WDL, the DocContents attribute, which is the part of source code that defines each executable, is now used for checksum calculation and comparison. However, since the CWL source code is packed as a nested JSON file (instead of standalone blocks in WDL), fragment applets and workflows will also include the code of all underlying processes in their DocContents, and they will not be reused if the wrapped applets/subworkflows have changed.
• CWL: Fix evaluating scatter inputs during workflow execution. It would no longer raise an error if optional inputs of the underlying task are not declared at the scatter level.
• CWL & WDL: Keep the Docker container after a task finishes running, so users can debug Docker related job failures.
• CWL: Fix to the pattern handling from secondaryFiles at workflow level during compilation

Dependency updates

wdlTools 0.17.11

• Keep the Docker container after a task finishes running, so users can debug Docker related job failures.
• Runtime object is aware if it was created with default system requirements

dxCommon 0.11.3

• Fix JsUtils.makeDeterministic to handle JsArrays sorting

cwlScala 0.8.3

• Updated cwljava with fixes to secondaryFiles with pattern field when parsing workflow-level parameters and the helper function utils.Uris.shortname to generate enum symbols without namespaces
• Updated cwljava to 1.0