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Version 2.5.0

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@nvnieuwk nvnieuwk released this 28 Aug 07:16
· 56 commits to master since this release
2.5.0
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Learn about vigilant mode.

⚠️ This version requires Nextflow version 25.04.0 or higher ⚠️

New features

  1. Added a new configuration option: validation.help.enumLength which sets the maximum length of enum values in the help message. The default is set to the value in the COLUMNS environment variable or 100 character if that variable isn't set.
  2. Added top-level schema description for detailed help --help <args>. If <args> is associated with a schema, then the top-level fields will be shown similarly to --help for the main schema (#146).
  3. Added a Troubleshooting and FAQ page to the documentation.

Changes

  1. The plugin now properly validates cloud storage files instead of skipping them. Exotic errors will be added to the error messages instead of failing the validation outright.
  2. Migrated to the new observer class in Nextflow 25.04.0
  3. Rework the deprecated paramsHelp() function to allow pipeline developers a fully fledged alternative to the help messages created via the configuration options. This change enables the use of dynamic help message with the strict configuration syntax introduced in Nextflow 25.04.0.
  4. Updated the error message when the JSON schema file is invalid to include the full file name.
  5. The ANSI log setting of Nextflow is now used to determine whether or not the log should be monochrome. This setting will take priority over the validation.monochromeLogs configuration option.
  6. Updated the examples in the examples directory and added automatic checking for validity of these examples.
  7. Refactored logic for parsing the jsonschema validation result into a new ValidationResult class.

Bug fixes

  1. CSV and TSV files with trailing commas or tabs will now be properly sanitized. This fixes issues with CSV and TSV files that contained empty header columns.
  2. Unidentified parameters are no longer printed out on failure of the parameter validation. This is to prevent a bug where all parameters would be printed out on failure.
  3. Fixed an issue where default values of null weren't being set correctly in samplesheetToList().
  4. Fixed an undocumented limit of 3MB for YAML format samplesheets (new limit is 50MB).
  5. Fixed issue where an empty string in a yaml for a file type string format would throw a Java error instead of reporting a proper validation error.

Logging configuration

This update contains a rework of the logging configuration. The validation.logging configuration scope has been added with options to replace and expand the current logging configuration options. These options can all take the following values:

  • skip: Skip logging
  • debug: Log debug messages (only printed in the .nextflow.log file)
  • info: Log info messages (also printed in the terminal)
  • warn: Log warning messages (also printed in the terminal, but in yellow)
  • error: Fail the pipeline and print the error message
Old option New option Description
validation.failUnrecognisedParams validation.logging.unrecognisedParams The logging level for unrecognised parameters.
validation.failUnrecognisedHeaders validation.logging.unrecognisedHeaders The logging level for unrecognised headers in samplesheets.
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