Merge pull request #47 from nextflow-io/fix/help-params

Fix help params being unexpected parameters

CHANGELOG.md

@@ -1,6 +1,14 @@
 # nextflow-io/nf-schema: Changelog
 
-# Version 2.1.0
+# 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
+
+# Version 2.1.0 - Tantanmen
 
 ## Breaking changes
 

README.md

@@ -25,7 +25,7 @@ Declare the plugin in your Nextflow pipeline configuration file:
 
 ```groovy title="nextflow.config"
 plugins {
-  id '[email protected].0'
+  id '[email protected].1'
 }
 ```
 

docs/parameters/help_text.md

@@ -5,7 +5,7 @@ Add the following configuration to your configuration files to enable the creati
 ```groovy title="nextflow.config"
 validation {
     help {
-        enabled: true
+        enabled = true
     }
 }
 ```

plugins/nf-schema/src/main/nextflow/validation/SchemaValidator.groovy

@@ -232,8 +232,8 @@ class SchemaValidator extends PluginExtensionPoint {
     // Initialise expected params if not present
     //
     Map initialiseExpectedParams(Map params) {
-        if( !params.containsKey("help") ) {
-            params.help = false
+        addExpectedParams().each { param ->
+            params[param] = false
         }
         return params
     }
@@ -244,7 +244,9 @@ class SchemaValidator extends PluginExtensionPoint {
     //
     List addExpectedParams() {
         def List expectedParams = [
-            "help"
+            config.help.shortParameter,
+            config.help.fullParameter,
+            config.help.showHiddenParameter
         ]
 
         return expectedParams
@@ -364,10 +366,9 @@ class SchemaValidator extends PluginExtensionPoint {
         Map options = [:],
         String command
     ) {
-        // TODO add link to help message migration guide once created
         if (!options.containsKey("hideWarning") || options.hideWarning == false) {
             log.warn("""
-Using `paramsHelp()` is not recommended. Check out the help message migration guide: <url>
+Using `paramsHelp()` is not recommended. Check out the help message migration guide: https://nextflow-io.github.io/nf-schema/latest/migration_guide/#updating-the-help-message
 If you intended to use this function, please add the following option to the input of the function:
     `hideWarning: true`
 

plugins/nf-schema/src/resources/META-INF/MANIFEST.MF

@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Id: nf-schema
-Plugin-Version: 2.1.0
+Plugin-Version: 2.1.1
 Plugin-Class: nextflow.validation.ValidationPlugin
 Plugin-Provider: nextflow
 Plugin-Requires: >=23.10.0