search

common-workflow-language / cwlviewer

A web application to view and share Common Workflow Language workflows
https://view.commonwl.org/
Apache License 2.0
45 stars 28 forks source link

correctly draw graph when a workflow level input & output share the same name #99

Closed mr-c closed 7 years ago

mr-c commented 7 years ago

https://view.commonwl.org/workflows/github.com/roryk/salmon-cwl/tree/master///salmon-workflow.cwl

See index in the linked workflow

MarkRobbo commented 7 years ago

@mr-c Is this valid as a workflow under the rules of salad-schema?

I had a similar issue #56 earlier and closed it due to a discussion that this is technically possible in cwltool but is actually considered not valid.

mr-c commented 7 years ago

Yes, this is valid and reasonable (a benefit of the scoping rules)

Pe 3 apr. 2017 18:17, "Mark Robinson" notifications@github.com a scris:

@mr-c https://github.com/mr-c Is this valid as a workflow under the rules of salad-schema?

I had a similar issue #56 https://github.com/common-workflow-language/cwlviewer/issues/56 earlier and closed it due to a discussion that this is technically possible in cwltool but is actually considered not valid https://github.com/common-workflow-language/schema_salad/issues/56.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/common-workflow-language/cwlviewer/issues/99#issuecomment-291175151, or mute the thread https://github.com/notifications/unsubscribe-auth/ABROCGk1LiD9lycmsHjHl_oAdgtn5mj4ks5rsQ2hgaJpZM4Mwhr1 .

MarkRobbo commented 7 years ago

@mr-c I would like some clarification on this issue. In the current version of schema salad/cwltool the following error is thrown due to the "index" ID being reused

object id `https://cdn.rawgit.com/roryk/salmon-cwl/9772782d041c4d0a180fc89d55c83c31b24bb6af/salmon-workflow.cwl#index` previously defined

Is this a bug in cwltool or is this no longer considered valid?

mr-c commented 7 years ago

Looks like the spec says "unique over the entire document", so an input and an output cannot share the same ID -- so I'll close this issue.