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CHANGELOG.md

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nextflow-io/nf-validation: Changelog

Version 1.1.4

Improvements

  • No longer does false validation on Azure and GCP cloud storage paths (#171)

Vulnerability fix

  • Updated the org.json package to version 20240303 (#172)

Version 1.1.3 - Asahikawa

Improvements

  • Added support for double quotes (") in CSV and TSV samplesheets (#134)

Version 1.1.2 - Wakayama

Bug fixes

  • Fixed an issue with inputs using file-path-pattern where only one file was found (Path casting to ArrayList error) (#132)

Version 1.1.1 - Shoyu

Bug fixes

  • Fixed an issue where samplesheet with a lot of null values would take forever to validate (#120) => Thanks @awgymer for fixing this!
  • Now YAML files are actually validated instead of skipped (#124)

Version 1.1.0 - Miso

Features

  • Add support for samplesheets with no header (#115)

Bug fixes

  • Floats and doubles should now be created when using the number type in the schema (#113)
  • When 0 is used as a default value in the schema, a 0 will now be used as the value in the .fromSamplesheet() channel instead of null (#114)

New features

  • Added file-path-pattern format to check every file fetched using a glob pattern. Using a glob is now also possible in the samplesheet and will create a list of all files found using that glob pattern. (#118)

Version 1.0.0 - Tonkotsu

The nf-validation plugin is now in production use across many pipelines and has (we hope) now reached a point of relative stability. The bump to major version v1.0.0 signifies that it is suitable for use in production pipelines.

This version also introduces a small breaking change of syntax when providing optional arguments to the functions. You can now provide optional arguments such as the nextflow parameters schema path as: validateParameters(parameters_schema: 'my_file.json')

(previous syntax used positional arguments instead).

Bug fixes

  • The path to a custom parameters schema must be provided through a map 'parameters_schema: 'my_file.json'' in validateParameters() and paramsSummaryMap() (#108)

Version 0.3.4

This version introduced a bug which made all pipeline runs using the function validateParameters() without providing any arguments fail.

This bug causes Nextflow to exit with an error on launch for most pipelines. It should not be used. It was removed from the Nextflow Plugin registry to avoid breaking people's runs.

Bug fixes

  • Do not check S3 URL paths with PathValidator FilePathValidator and DirectoryPathValidator (#106)
  • Make monochrome_logs an option in paramsSummaryLog(), paramsSummaryMap() and paramsHelp() instead of a global parameter (#101)

Version 0.3.3

Bug fixes

  • Do not check if S3 URL paths exists to avoid AWS errors, and add a new parameter validationS3PathCheck (#104)

Version 0.3.2

Bug fixes

  • Add parameters defined on the top level of the schema and within the definitions section as expected params (#79)
  • Fix error when a parameter is not present in the schema and evaluates to false (#89)
  • Changed the schema_filename option of fromSamplesheet to parameters_schema to make this option more clear to the user (#91)

Version 0.3.1

Bug fixes

  • Don't check if path exists if param is not true (#74)
  • Don't validate a file if the parameter evaluates to false (#75)

Version 0.3.0

New features

  • Check that a sample sheet doesn't have duplicated entries by default. Can be disabled with --validationSkipDuplicateCheck (#72)

Bug fixes

  • Only validate a path if it is not null (#50)
  • Only validate a file with a schema if the file path is provided (#51)
  • Handle errors when sample sheet not provided or doesn't have a schema (#56)
  • Silently ignore samplesheet fields that are not defined in samplesheet schema (#59)
  • Correctly handle double-quoted fields containing commas in csv files by .fromSamplesheet() (#63)
  • Print param name when path does not exist (#65)
  • Fix file or directory does not exist error not printed when it was the only error in a samplesheet (#65)
  • Do not return parameter in summary if it has no default in the schema and is set to 'false' (#66)
  • Skip the validation of a file if the path is an empty string and improve error message when the path is invalid (#69)

Deprecated

  • The meta map of input channels is not an ImmutableMap anymore (#68). Reason: Issue #52

Version 0.2.1

Bug fixes

  • Fixed a bug where immutable_meta option in fromSamplesheet() wasn't working when using validateParameters() first. (@nvnieuwk)

Version 0.2.0

New features

  • Added a new documentation site. (@ewels and @mashehu)
  • Removed the file-path-exists, directory-path-exists and path-exists and added a exists parameter to the schema. (@mirpedrol)
  • New errorMessage parameter for the schema which can be used to create custom error messages. (@mirpedrol)
  • Samplesheet validation now happens in validateParameters() using the schema specified by the schema parameter in the parameters schema. (@mirpedrol)

Improvements

  • The meta maps are now immutable by default, see ImmutableMap for more info (@nvnieuwk)
  • validateAndConvertSamplesheet() has been renamed to fromSamplesheet()
  • Refactor --schema_ignore_params to --validationSchemaIgnoreParams

Bug fixes

  • Fixed a bug where an empty meta map would be created when no meta values are in the samplesheet schema. (@nvnieuwk)

Version 0.1.0

Initial release.