Merge pull request #78 from nextflow-io/fix/defaultIgnoreParams

fix ignore configs not working

Author: nvnieuwk

CHANGELOG.md

@@ -1,10 +1,11 @@
 # nextflow-io/nf-schema: Changelog
 
-# Version 2.3.0
+# Version 2.2.1
 
 ## Bug fixes
 
 1. Fixed a bug in `paramsSummaryMap()` related to the processing of workflow config files.
+2. Fixed a bug where `validation.defaultIgnoreParams` and `validation.ignoreParams` would not actually ignore the parameter validation.
 
 # Version 2.2.0 - Kitakata
 

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

@@ -330,8 +330,12 @@ class SchemaValidator extends PluginExtensionPoint {
         // Validate
         List<String> validationErrors = validator.validate(paramsJSON, schema_string)
         this.errors.addAll(validationErrors)
-        if (this.hasErrors()) {
-            def msg = "${colors.red}The following invalid input values have been detected:\n\n" + errors.join('\n').trim() + "\n${colors.reset}\n"
+        def List<String> modifiedIgnoreParams = config.ignoreParams.collect { param -> "* --${param}" as String }
+        def List<String> filteredErrors = errors.findAll { error -> 
+            return modifiedIgnoreParams.find { param -> error.startsWith(param) } == null
+        }
+        if (filteredErrors.size() > 0) {
+            def msg = "${colors.red}The following invalid input values have been detected:\n\n" + filteredErrors.join('\n').trim() + "\n${colors.reset}\n"
             log.error("Validation of pipeline parameters failed!")
             throw new SchemaValidationException(msg, this.getErrors())
         }

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

@@ -52,6 +52,5 @@ class ValidationConfig {
         }
         ignoreParams += config.defaultIgnoreParams ?: []
         ignoreParams += 'nf_test_output' //ignore `nf_test_output` directory when using nf-test
-
     }
 }

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

@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Id: nf-schema
-Plugin-Version: 2.2.0
+Plugin-Version: 2.2.1
 Plugin-Class: nextflow.validation.ValidationPlugin
 Plugin-Provider: nextflow
 Plugin-Requires: >=23.10.0

plugins/nf-schema/src/test/nextflow/validation/ValidateParametersTest.groovy

@@ -483,6 +483,33 @@ class ValidateParametersTest extends Dsl2Spec{
         !stdout
     }
 
+    def 'should ignore wrong expected params' () {
+        given:
+        def schema = Path.of('src/testResources/nextflow_schema.json').toAbsolutePath().toString()
+        def SCRIPT = """
+            params.input = 1
+            params.outdir = 2
+            include { validateParameters } from 'plugin/nf-schema'
+            
+            validateParameters(parameters_schema: '$schema')
+        """
+
+        when:
+        def config = ["validation": [
+            "ignoreParams": ['input'],
+            "defaultIgnoreParams": ['outdir']
+        ]]
+        def result = new MockScriptRunner(config).setScript(SCRIPT).execute()
+        def stdout = capture
+                .toString()
+                .readLines()
+                .findResults {it.contains('WARN nextflow.validation.SchemaValidator') || it.startsWith('* --') ? it : null }
+
+        then:
+        noExceptionThrown()
+        !stdout
+    }
+
     def 'should fail for unexpected param' () {
         given:
         def schema = Path.of('src/testResources/nextflow_schema.json').toAbsolutePath().toString()