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Schema: Write future reference schema #2748

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Tracked by #2429
ewels opened this issue Feb 14, 2024 · 1 comment
Open
Tracked by #2429

Schema: Write future reference schema #2748

ewels opened this issue Feb 14, 2024 · 1 comment
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@ewels
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ewels commented Feb 14, 2024

We have plans for several extensions to the Nextflow parameter schema format.

To allow multiple groups to work in parallel, it would be good to manually write "the most complex schema possible" that we imagine supporting once those tasks are done. This way, we have a common reference point for where we expect to get to later in the year.

@ewels ewels changed the title Write reference schema to aim for Schema: Write future reference schema Feb 14, 2024
@ewels ewels added the schema label Feb 14, 2024
@nvnieuwk
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nf-validation adds validation support for following keys as an extension on top of draft 2020-12:

  • exists => Boolean: checks if a file/directory exists (true) or does not exist (false)
  • format:
    • directory-path => The string should be a directory, not a file
    • file-path => The string should be a file, not a directory
    • path => The string should be a file or directory
    • file-path-pattern => The string is a glob pattern that should resolve in at least one file
  • schema => String: The schema that will be used to validate the file given in this field
  • uniqueEntries => List: A list of entries that should form a unique combination

Following fields were added as annotation fields (so no influence on validation, but can be used in other parts of the code):

  • meta => String or List: This field should be added to the meta map in the output channel (only used in samplesheet schemas)
  • description => String: The description of the field (used in the help message)
  • help_text => String: Additional text to be displayed in the help message
  • errorMessage => String: Custom error message to be displayed in case of a validation error in this field

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