Common Workflow Language

Description about the CWL project, how some of the concepts map and limitations in the implementation.

Equivalents

  • How do I specify an Array from types?

By wrapping the data_type by an Array, for example: String -> Array(String). Nb: the Array type must be imported from janis_core.

  • What’s the equivalent for ``InitialWorkDirRequirement``?

You can add localise_file=True to your ToolInput. This is well defined for individual files in CWL and WDL. here is no equivalent for writable, though suggestions are welcome. Although the localise_file attribute is allowed for Array data types, the WDL translation will become disabled as this behaviour is not well defined.

From v1.1/CommandLineTool:

If the same File or Directory appears more than once in the InitialWorkDirRequirement listing, the implementation must choose exactly one value for path; how this value is chosen is undefined.
  • What’s the equivalent for ``EnvVarRequirement`` / how do I ensure environment variables are set in my execution environment?

You can include the following code block within your CommandTool:

# Within CommandTool

def env_vars(self):
   return {
       "myvar1": InputSelector("myInput"),
       "myvar2": "constantvalue"
   }