search

PMCC-BioinformaticsCore / janis-core

Core python modules for Janis Pipeline workflow assistant
GNU General Public License v3.0
4 stars 9 forks source link

CWL generation: fix stdout #96

Closed mr-c closed 3 years ago

mr-c commented 3 years ago

Fixes #95

illusional commented 3 years ago

Thanks @mr-c, these expressions are a little tricky, like WDL, we allow you to include stdout / stderr as files in the expression, so effectively self in the expression becomes [_stdout, _stderr], and Janis knows that Stdout in the output expression is self[0]. It's not great, but it seems to have worked so far.

I've created a follow-on PR to this to better address your issue.