Releases: nextflow-io/nf-schema
Releases · nextflow-io/nf-schema
Version 2.1.1
Bug fixes
- The help parameters are now no longer unexpected parameters when validating parameters.
- Fixed a typo in the docs
- Added a URL to the help message migration docs to the
paramsHelp()
deprecation message - The old
validation.showHiddenParams
config option works again to ensure backwards compatibility. Usingvalidation.help.showHidden
is still preffered and the old option will emit a deprecation message. - Resolved an issue where the UniqueEntriesEvaluator did not correctly detect non-unique combinations.
Version 2.1.0 - Tantanmen
Breaking changes
- The minimum supported Nextflow version is now
23.10.0
instead of22.10.0
New features
- The plugin now fully supports nested parameters!
- Added a config option
validation.parametersSchema
which can be used to set the parameters JSON schema in a config file. The default isnextflow_schema.json
- The parameter summary log will now automatically show nested parameters.
- Added two new configuration options:
validation.summary.beforeText
andvalidation.summary.afterText
to automatically add some text before and after the output of theparamsSummaryLog()
function. The colors from these texts will be automatically filtered out ifvalidation.monochromeLogs
is set totrue
.
Help message changes
- 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 useparamsHelp()
for some reason in your pipeline, please add thehideWarning:true
option to it to make sure the deprecation warning will not be shown. - 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 thehidden: true
keyword in the schema. Default =showHidden
validation.help.showHidden
: Set this totrue
to show hidden parameters by default. This configuration option is overwritten by the value supplied to the parameter invalidation.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 ifvalidation.monochromeLogs
is set totrue
.validation.help.afterText
: Some custom text to add after the help message. The colors from this text will be automatically filtered out ifvalidation.monochromeLogs
is set totrue
.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 ifvalidation.monochromeLogs
is set totrue
.
- 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
) - The help message now won't show empty parameter groups.
- The help message will now automatically contain the three parameters used to get help messages.
JSON schema fixes
- The
defs
keyword is now deprecated in favor of the$defs
keyword. This to follow the JSON schema guidelines. We will continue supportingdefs
for backwards compatibility.
Version 2.0.1
Vulnerability fix
- 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 thesample
andreplicate
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 ofnf-validation
v2.0 😁
Changes
- Changed the used draft for the schema from
draft-07
todraft-2020-12
. See the 2019-09 and 2020-12 release notes for all changes (#141) - Removed the
fromSamplesheet
channel operator and added asamplesheetToList
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 useuniqueItems
oruniqueEntries
instead (#141) - Removed the
skip_duplicate_check
option from thesamplesheetToList()
function and the--validationSkipDuplicateCheck
parameter. You should now use theuniqueEntries
oruniqueItems
keywords in the schema instead (#141) samplesheetToList()
now does dynamic typecasting instead of using thetype
fields in the JSON schema. This is done due to the complexity ofdraft-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 infalse
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