This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
Syntax change in Cromwell v29 command line
Heads up! The upcoming version 29 of Cromwell will include a breaking change in the command line syntax. Full details will be provided in the release notes when Cromwell 29 is ready for primetime; in the meantime the gist is that we're moving away from positional inputs in favor of explicit arguments. So for example this simple execution command:
java -jar Cromwell.jar run myWorkflow.wdl myWorkflow_inputs.json
will change to the more explicit:
java -jar Cromwell.jar run myWorkflow.wdl --inputs myWorkflow_inputs.json
The code changes can be viewed here for those who are into that level of detail.
We plan to update usage examples and relevant instructions in the WDL documentation materials at the time the new version is released, and will add a note regarding versions where appropriate for anyone still using a version anterior to 29. Note that there may be a short lag between the release and the documentation updates; we'll try to keep it to a minimum.