Output files in the input directory

Question

[thomas.e]

Hello,

I'm using snver which creates its output next to the input files, not in the directory where the program is running. There are no options to control this. I've been racking my brain for 1.5 days to figure out how can I can gather that output. The only thing I've found is a vague post suggesting that this is not supported by CWL.

Thanks, Evan.

[GenoMax]

This is a question about cwl and has been correctly tagged.

[thomas.e]

Thanks - although I did tag it as CWL when I submitted it.

[GenoMax]

You did the right thing. People overlook cwl tag and may start providing suggestions outside of cwl so I added that explicit note.

Answer 1

[Michael R. Crusoe]

Hello thomas.e,

This is very much supported by CWL!

See http://www.commonwl.org/user_guide/15-staging/ to learn how to stage your input files into the working directory.

Cheers,

[thomas.e]

Perfect, thanks! (Ensure this value has at least 20 characters (it has 16).

[ngoc.nguyen]

Yes, I can stage input files into the working directory and write output files to the working directory. But, is it possible to stage a directory with input files in it and be able to write the output files to that directory? When I try to write to staged directory, I get:

cannot create regular file '...': Read-only file system

Thanks, Ngoc

[Michael R. Crusoe]

Hello @ngoc.nguyen, I just saw your comment.

Yes, you'll need to set writable: true when using InitialWorkDirRequirement

We haven't written the user guide entry for that yet, if you would like to see that then a comment or a 👍 on https://github.com/common-workflow-language/user_guide/issues/36 will help us prioritize that.