Question: CWL question: File location vs path
0
gravatar for wolfganggerlach1981
2.6 years ago by
USA/Chicago/Argonne National Laboratory
wolfganggerlach198150 wrote:

For the object File the CWL documentation says:

If the location field is not provided, the contents field must be provided. The implementation must assign a unique identifier for the location field.

What when I use path instead of location? I assume the contents field does not have to be provided ?!

cwl • 926 views
ADD COMMENTlink modified 2.6 years ago by Michael R. Crusoe1.8k • written 2.6 years ago by wolfganggerlach198150
1

What are you talking about? "The object File" is about a vague as anything can be.

ADD REPLYlink written 2.6 years ago by karl.stamm3.6k
2

This question is for "cwl" (common workflow language) developers. They use Biostars as their official support channel. The question has been appropriately tagged with "cwl" tag.

ADD REPLYlink written 2.6 years ago by genomax78k
1
gravatar for Michael R. Crusoe
2.6 years ago by
Common Workflow Language project
Michael R. Crusoe1.8k wrote:

Hello wolfganggerlach1981,

http://www.commonwl.org/v1.0/CommandLineTool.html#File

This depends on the context. As a user providing an input object, they only need to supply one of path, location, or contents.

A CWL implementation needs to derive all the remaining fields so that they are available to parameter references or inline Javascript.

A. If only the contents of the File is provided then a URI must be generated at some point to be the location and the File should end up on an accessible path as well. From the path the basename, dirname, nameroot, and nameext must be derived.

B. If only the path is provided then that can be turned into a location URI. The lazy way is by prepending file://, or an implementation might assign an internally relevant URI like shock://[…] :-) Like in situation A, the remaining fields are to be generated from the path

C. If only the location is provided then that File should end up on an accessible POSIX path as well. Like in situation A, the remaining fields are to be generated from the path

ADD COMMENTlink written 2.6 years ago by Michael R. Crusoe1.8k
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