search

EOSC-LOFAR / prefactor-cwl

CWL version of prefactor
MIT License
3 stars 3 forks source link

Add formats (also unofficial ones) and labels for outputs #15

Closed tammojan closed 6 years ago

tammojan commented 6 years ago

As I understand it, the use of non-standard values for format is allowed if $schemas is left empty. Should I remove $schemas where we use numpy or h5parm as format?

tammojan commented 6 years ago

I think I addressed all your comments.

mr-c commented 6 years ago

This will be mergeable once make run works

tammojan commented 6 years ago

I'm afraid I got stuck. make run complains about the format:

Cannot make scatter job: Missing required 'format' for File {'basename': 'calibrated.MS', 'nameroot': 'calibrated', 'class': 'Directory', 'nameext': '.MS', 'location': 'file:///Users/dijkema/opt/prefactor-cwl/cache/7b562cc0052ac22467f68a769dc4e2c5/calibrated.MS'}

However, I've added the format to both the step that produces the output calibrated.MS: ndppp-prep-cal.cwl and to the step that needs calibrated.MS as input: sky_cal .

mr-c commented 6 years ago

@tammojan did you re-run make no-singularity to pick up your changes?

tammojan commented 6 years ago

Yes I did.

mr-c commented 6 years ago

Ah, that is an unhelpful error message. format is not valid for type: Directory, only type: File

tammojan commented 6 years ago

That means that I should remove it for all Measurement Sets I suppose (because a Measurement Set is a directory).

mr-c commented 6 years ago

That means that I should remove it for all Measurement Sets I suppose (because a Measurement Set is a directory).

Yes.

I made an issue in cwltool to catch this sooner: https://github.com/common-workflow-language/cwltool/issues/607