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nextflow-io/nf-schema: Changelog

Version 2.2.1

Bug fixes

  1. Fixed a bug in paramsSummaryMap() related to the processing of workflow config files.
  2. Fixed a bug where validation.defaultIgnoreParams and validation.ignoreParams would not actually ignore the parameter validation.

Version 2.2.0 - Kitakata

New features

  1. Added a new configuration option validation.failUnrecognisedHeaders. This is the analogue to failUnrecognisedParams, but for samplesheet headers. The default is false which means that unrecognized headers throw a warning instead of an error.
  2. Added a new configuration option validation.summary.hideParams. This option takes a list of parameter names to hide from the parameters summary created by paramsSummaryMap() and paramsSummaryLog()

Bug fixes

  1. Fixed a bug in samplesheetToList that caused output mixing when the function was used more than once in channel operators.
  2. Added a missing depencency for email format validation.
  3. All path formats (with exception to file-path-pattern) will now give a proper error message when a file-path-pattern has been used.

Improvements

  1. Improved the exists keyword documentation with a warning about an edge case.
  2. Updated the error messages. Custom error messages provided in the JSON schema will now be appended to the original error messages instead of overwriting them.

Version 2.1.2

Bug fixes

  1. The directory nf_test_output is now an ignored parameter during validation to support use of both nf_test and nf_schema.
  2. uniqueEntries will now skip unique checks when all values in the requested array properties are empty. This had to be implemented to allow optional values to work with the uniqueEntries check. Partially filled in array properties will still fail (and that's how it's meant to be). Be sure to use oneOf to properly configure all possible combinations in case this causes some issues.
  3. Improved the error messages produced by uniqueEntries.

Documentation

  1. Fix some faults in the docs

Version 2.1.1

Bug fixes

  1. The help parameters are now no longer unexpected parameters when validating parameters.
  2. Fixed a typo in the docs
  3. Added a URL to the help message migration docs to the paramsHelp() deprecation message
  4. The old validation.showHiddenParams config option works again to ensure backwards compatibility. Using validation.help.showHidden is still preffered and the old option will emit a deprecation message.
  5. Resolved an issue where the UniqueEntriesEvaluator did not correctly detect non-unique combinations.

Version 2.1.0 - Tantanmen

Breaking changes

  1. The minimum supported Nextflow version is now 23.10.0 instead of 22.10.0

New features

  1. The plugin now fully supports nested parameters!
  2. Added a config option validation.parametersSchema which can be used to set the parameters JSON schema in a config file. The default is nextflow_schema.json
  3. The parameter summary log will now automatically show nested parameters.
  4. Added two new configuration options: validation.summary.beforeText and validation.summary.afterText to automatically add some text before and after the output of the paramsSummaryLog() function. The colors from these texts will be automatically filtered out if validation.monochromeLogs is set to true.

Help message changes

  1. The use of the paramsHelp() function has now been deprecated in favor of a new built-in help message functionality. paramsHelp() has been updated to use the reworked help message creator. If you still want to use paramsHelp() for some reason in your pipeline, please add the hideWarning:true option to it to make sure the deprecation warning will not be shown.
  2. Added new configuration values to support the new help message functionality:
    • validation.help.enabled: Enables the checker for the help message parameters. The plugin will automatically show the help message when one of these parameters have been given and exit the pipeline. Default = false
    • validation.help.shortParameter: The parameter to use for the compact help message. This help message will only contain top level parameters. Default = help
    • validation.help.fullParameter: The parameter to use for the expanded help message. This help message will show all parameters no matter how deeply nested they are. Default = helpFull
    • validation.help.showHiddenParameter: The parameter to use to also show all parameters with the hidden: true keyword in the schema. Default = showHidden
    • validation.help.showHidden: Set this to true to show hidden parameters by default. This configuration option is overwritten by the value supplied to the parameter in validation.help.showHiddenParameter. Default = false
    • validation.help.beforeText: Some custom text to add before the help message. The colors from this text will be automatically filtered out if validation.monochromeLogs is set to true.
    • validation.help.afterText: Some custom text to add after the help message. The colors from this text will be automatically filtered out if validation.monochromeLogs is set to true.
    • validation.help.command: An example command to add to the top of the help message. The colors from this text will be automatically filtered out if validation.monochromeLogs is set to true.
  3. Added support for nested parameters to the help message. A detailed help message using --help <parameter> will now also contain all nested parameters. The parameter supplied to --help can be a nested parameter too (e.g. --help top_parameter.nested_parameter.deeper_parameter)
  4. The help message now won't show empty parameter groups.
  5. The help message will now automatically contain the three parameters used to get help messages.

JSON schema fixes

  1. The defs keyword is now deprecated in favor of the $defs keyword. This to follow the JSON schema guidelines. We will continue supporting defs for backwards compatibility.

Version 2.0.1 - Tsukemen

Vulnerability fix

  1. Updated the org.json package to version 20240303.

Version 2.0.0 - Kagoshima

To migrate from nf-validation please follow the migration guide

New features

  • Added the uniqueEntries keyword. This keyword takes a list of strings corresponding to names of fields that need to be a unique combination. e.g. uniqueEntries: ['sample', 'replicate'] will make sure that the combination of the sample and replicate fields is unique. (#141)
  • Added samplesheetToList which is the function equivalent of .fromSamplesheet #3
  • Added a warning if the nf-schema version is unpinned. Let's hope this prevents future disasters like the release of nf-validation v2.0 😁

Changes

  • Changed the used draft for the schema from draft-07 to draft-2020-12. See the 2019-09 and 2020-12 release notes for all changes (#141)
  • Removed the fromSamplesheet channel operator and added a samplesheetToList function instead. This function validates the samplesheet and returns a list of it. #3
  • Removed the unique keyword from the samplesheet schema. You should now use uniqueItems or uniqueEntries instead (#141)
  • Removed the skip_duplicate_check option from the samplesheetToList() function and the --validationSkipDuplicateCheck parameter. You should now use the uniqueEntries or uniqueItems keywords in the schema instead (#141)
  • samplesheetToList() now does dynamic typecasting instead of using the type fields in the JSON schema. This is done due to the complexity of draft-2020-12 JSON schemas. This should not have that much impact but keep in mind that some types can be different between this version and older versions in nf-validation (#141)
  • samplesheetToList() will now set all missing values as [] instead of the type specific defaults (because of the changes in the previous point). This should not change that much as this will also result in false when used in conditions. (#141)
  • Removed the configuration parameters and added configuration options instead. For a full list of these new options, please have a look at the configuration docs
  • Ignore validation of Azure and GCP hosted blob storage files in addition to AWS S3 hosted files. This is because they are not true POSIX compliant files and would incorrectly fail validation (#29)

Improvements

  • Setting the exists keyword to false will now check if the path does not exist (#141)
  • The schema keyword will now work in all schemas. (#141)
  • Improved the error messages (#141)
  • .fromSamplesheet() now supports deeply nested samplesheets (#141)