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WDL structs are not handled #72
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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 Any pointers on how this could be fixed? Would it be creating Thanks! |
🙃😀
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.
Thank you! |
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: type:
type: record
name: references
items:
- id: genome_fa
type: File
- id: annotation_gtf
type: File |
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#L3Referencing 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
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