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. There 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"
}