WDL structs are not handled

[dinithiW]

Currently, WDL specific custom compound type struct is not translated by the translator (https://github.com/openwdl/wdl/blob/main/versions/1.1/SPEC.md#custom-types-structs)

In WDL documents, after the definition of these structs, they can be referenced in the input, output and command sections. A workflow using struct type is shown in the this link. https://github.com/broadinstitute/warp/blob/b3f5c898d1b535aaca8dc9e9f4223697a7a0a9a9/pipelines/skylab/build_indices/BuildIndices.wdl#L3

Referencing in input section: https://github.com/broadinstitute/warp/blob/b3f5c898d1b535aaca8dc9e9f4223697a7a0a9a9/pipelines/skylab/build_indices/BuildIndices.wdl#L52
Referencing in output section: https://github.com/broadinstitute/warp/blob/b3f5c898d1b535aaca8dc9e9f4223697a7a0a9a9/pipelines/skylab/build_indices/BuildIndices.wdl#L126
Referencing in command section: https://github.com/broadinstitute/warp/blob/b3f5c898d1b535aaca8dc9e9f4223697a7a0a9a9/pipelines/skylab/build_indices/BuildIndices.wdl#L68

[kinow]

I cloned the repository and read the README and parts of the code today. Then decided to choose a random WDL from the warp repository, and chose exactly the build_indices mentioned above. Had the error when trying to translate it, and searched in the issues, finding this one 😬

Any pointers on how this could be fixed? Would it be creating InputRecordSchema's and OutputRecordSchemas?

Thanks!
Bruno

[mr-c]

I cloned the repository and read the README and parts of the code today. Then decided to choose a random WDL from the warp repository, and chose exactly the build_indices mentioned above. Had the error when trying to translate it, and searched in the issues, finding this one 😬

🙃😀

Any pointers on how this could be fixed? Would it be creating InputRecordSchema's and OutputRecordSchemas?

That is what I would do. Feel free to focus on solving the issue of how WDL struts are used in just one of the examples, versus making the perfect solution all at once.

Thanks!
Bruno

Thank you!

[mr-c]

For CWL use https://www.commonwl.org/v1.2/CommandLineTool.html#CommandInputRecordSchema , https://www.commonwl.org/v1.2/CommandLineTool.html#CommandOutputRecordSchema for CommandLineTools and https://www.commonwl.org/v1.2/Workflow.html#InputRecordSchema , https://www.commonwl.org/v1.2/Workflow.html#OutputRecordSchema for workflows

Conversion of one of the examples:
https://github.com/broadinstitute/warp/blob/b3f5c898d1b535aaca8dc9e9f4223697a7a0a9a9/pipelines/skylab/build_indices/BuildIndices.wdl#L3

type:
   type: record
   name: references
   items:
      - id: genome_fa
        type: File
      - id: annotation_gtf
        type: File