Version 2.4.2

Bug fixes

1. validateParameters should now correctly ignore nested parameters given in the validation.ignoreParams and the validation.defaultIgnoreParams configuration options.

Version 2.4.1

Bug fixes

1. Allow GString values for all configuration options that allow String values.

Version 2.4.0

New features

1. Added a new configuration option: validation.maxErrValSize which sets the maximum length that a value in an error message can be. The default is set to 150 characters.
2. Added a new function: validate() that can be used to validate any data structure using a JSON schema.

Bug fixes

1. Move the unpinned version check to an observer. This makes sure the warning is always shown and not only when importing a function.
2. Added a missing inherited method to the observer to fix issues with workflow output publishing
3. Fixed unexpected failures with samplesheet schemas using anyOf, allOf and oneOf
4. Fixed an error with help messages when the type keyword was missing
5. Fix compilation errors in Java 21

Improvements

1. Slow uniqueness check (> 2hrs for 100k samples) made 400x faster by switching from findAll to a subMap for isolating the required unique fields.
2. patternProperties now has greater support, with no warnings about invalid parameters which actually match a pattern
3. Added better error handling and debug messages to the configuration parser.

Changes

1. Refactored the whole codebase to make future development easier
2. Bumped the minimal Nextflow version to 24.10.0

Version 2.3.0 - Hakodate

Bug fixes

1. The help message will now also be printed out when no functions of the plugin get included in the pipeline.
2. JSON and YAML files that are not a list of values should now also be validated correctly. (Mind that samplesheets always have to be a list of values to work with samplesheetToList)

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

Vulnerability fix

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