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Use a controlled vocabulary when linting input and output types in meta.yml #1553

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mahesh-panchal opened this issue May 9, 2022 · 2 comments · Fixed by #2190
Closed

Use a controlled vocabulary when linting input and output types in meta.yml #1553

mahesh-panchal opened this issue May 9, 2022 · 2 comments · Fixed by #2190

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@mahesh-panchal
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Description of feature

There are parts of the meta.yml that don't have a clear specification.
For example

input:
...
  - sdf:
      type: folder/file
      description: The SDF (RTG Sequence Data File) of the reference genome. Can be a folder or a tar-zipped folder.
      pattern: "*.{,tar.gz}"

input.sdf.type should probably use a controlled vocabulary, but it's currently uncontrolled.

It would be nice if
nf-core modules lint validated the type using a controlled vocabulary.

@mirpedrol mirpedrol linked a pull request Mar 9, 2023 that will close this issue
@jfy133
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jfy133 commented Jun 18, 2023

I think this has been addressed now right @mashehu @mirpedrol ? We have fixed input types I believe?

@mashehu
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mashehu commented Jun 18, 2023

Correct, the yaml-schema checks that now.

@mashehu mashehu closed this as completed Jun 18, 2023
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3 participants