Open zymergen-mbarton opened 4 years ago
Hi @zymergen-mbarton thank you for reporting this issue and sorry you are having problems. Would it be possible to share the workflow? We can do this via the SB issues system (or you can mail me directly) if this is acceptable. Otherwise, would it be possible to share some notable features of the workflow code, so that we can track down why this may be happening? Thank you!
cc: @bogdang989
Thanks @kaushik-work for responding so quickly, your prompt replies are much appreciated. I can't share the workflow here unfortunately, however I will email separately.
As for notable features, a potential reproducible test case might be exporting a workflow with a couple of tools using prefix
and separate
arguments, and also containing expression
types too. I mention expressions because I also saw another error after manually editing fixes for the errors around prefix
and separate
to see if that solved the issue. This error seemed to be about the closing of the JS expression.
ERROR I'm sorry, I couldn't load this CWL file, try again with --debug for more information.
The error was: Substitution error, unfinished block starting at position 1: ${
I have a relatively large workflow that I have created using rabix composer and then exported to YAML using both the command line rabix composer and the Seven Bridges web editor. In both cases I get an error when running
cwltool --validate
on the exported file. The errors appear to be related to unexpected fields. For example:The offending fields appear to be
prefix
andseparate
.I wonder if you have any suggestions on how to generate a valid cwl file from exporting a workflow created in rabix composer? Thank you.