- CWL: All tasks and workflows conformance tests now pass
- CWL: Allow a valid CWL identifier that starts with a number or other characters disallowed by the DNAnexus platform
- Valid CWL IDs starting with disallowed characters will be padded with an extra "___" when generating the full encoded name, which will still be a valid CWL ID (as an URI) when decoded
- CWL: Fix to an error with execution of nested workflow step due to incorrect step identifiers. Previously it prevented running of workflows with the
--single-processflag. - WDL: Minor fixes with directory path handling when passing
-separateOutputsflag- When a workflow was compiled with the -separateOutputs flag, it would result in an error at runtime saying "InvalidInput: Folder path must start with /."
- WDL: Fix an issue with optional identifiers not found when they were a part of an unused expression
- Fix an issue where a
dbclusterobject stored in a project in which a workflow was run was causing a runtime error, if the workflow was compiled with the-reorgflag.
Dependency updates
dxApi 0.13.2
- Added database and dbcluster to the list of DNAnexus data objects that are recognized and can be described
dxFileAccessProtocols 0.5.4
- Fix to the issue where
-separateOutputsoption was causing a dx API runtime error due to a missing leading/in folder path
wdlTools 0.17.8
- Input variables are now evaluated and added to the dependency graph, even when they are optional and not used. They need to be a part of the graph in the case when they are assigned to other (unused) variables for a proper expression evaluation.