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Stdout / Stderr are currently types in Janis, but in reality they're probably better as selectors with type File. Being a Selector means they will better participate in operations (like .contents()) or maybe a suggested new .read_json() -> then an index operator could be used.
This would be useful when converting CWL in the cases of ExpressionTool or a commandlinetool that declares the stdout: cwl.output.json (without an outputBinding pattern).
WDL -> stdout()
CWL -> File should have path _stdout which you could collect with glob, or manually construct using path / basname
Maybe even making it an operator. You end up the CWL expression of self[0] to represent the glob order from here:
Stdout / Stderr are currently types in Janis, but in reality they're probably better as selectors with type File. Being a Selector means they will better participate in operations (like
.contents()
) or maybe a suggested new.read_json()
-> then an index operator could be used.This would be useful when converting CWL in the cases of ExpressionTool or a commandlinetool that declares the
stdout: cwl.output.json
(without an outputBinding pattern).stdout()
_stdout
which you could collect with glob, or manually construct using path / basnameMaybe even making it an operator. You end up the CWL expression of
self[0]
to represent the glob order from here:janis-core/janis_core/translations/cwl.py
Lines 1312 to 1318 in 96718bc
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