Merge pull request #49 from nextflow-io/more-patch-fixes

More patch fixes

Author: nvnieuwk

CHANGELOG.md

@@ -7,7 +7,8 @@
 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. Resolved an issue where the UniqueEntriesEvaluator did not correctly detect non-unique combinations.
+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
 

docs/migration_guide.md

@@ -284,8 +284,8 @@ The creation of the help message now needs to be enabled in the configuration fi
     ```groovy title="nextflow.config"
     validation {
         help {
-            enabled: true
-            command: "nextflow run my_pipeline --input input_file.csv"
+            enabled = true
+            command = "nextflow run my_pipeline --input input_file.csv"
         }
     }
     ```

plugins/nf-schema/src/main/nextflow/validation/config/HelpConfig.groovy

@@ -26,7 +26,7 @@ class HelpConfig {
     final public String  command
     final public Boolean showHidden
 
-    HelpConfig(Map map, Map params, Boolean monochromeLogs) {
+    HelpConfig(Map map, Map params, Boolean monochromeLogs, Boolean showHiddenParams) {
         def config = map ?: Collections.emptyMap()
         enabled             = config.enabled                    ?: false
         shortParameter      = config.shortParameter             ?: "help"
@@ -41,6 +41,6 @@ class HelpConfig {
             afterText   = config.afterText  ?: ""
             command     = config.command    ?: ""
         }
-        showHidden          = params.get(showHiddenParameter)   ?: config.showHidden    ?: false
+        showHidden          = params.containsKey(showHiddenParameter) ? params.get(showHiddenParameter) : config.showHidden    ?: showHiddenParams ?: false
     }
 }

plugins/nf-schema/src/main/nextflow/validation/config/ValidationConfig.groovy

@@ -22,7 +22,7 @@ class ValidationConfig {
     final public Boolean monochromeLogs
     final public Boolean failUnrecognisedParams
     final public String  parametersSchema
-    final public Boolean showHiddenParams = false
+    final public Boolean showHiddenParams
     final public HelpConfig help
     final public SummaryConfig summary
 
@@ -33,11 +33,12 @@ class ValidationConfig {
         lenientMode             = config.lenientMode            ?: false
         monochromeLogs          = config.monochromeLogs         ?: false
         failUnrecognisedParams  = config.failUnrecognisedParams ?: false
-        if(config.showHiddenParams) {
+        showHiddenParams        = config.showHiddenParams       ?: false
+        if(config.containsKey("showHiddenParams")) {
             log.warn("configuration option `validation.showHiddenParams` is deprecated, please use `validation.help.showHidden` or the `--showHidden` parameter instead")
         }
         parametersSchema        = config.parametersSchema       ?: "nextflow_schema.json"
-        help                    = new HelpConfig(config.help as Map ?: [:], params, monochromeLogs)
+        help                    = new HelpConfig(config.help as Map ?: [:], params, monochromeLogs, showHiddenParams)
         summary                 = new SummaryConfig(config.summary as Map ?: [:], monochromeLogs)
 
         if(config.ignoreParams && !(config.ignoreParams instanceof List<String>)) {