Fall back to nextflow_schema.json types for CLI param coercion

modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy

@@ -39,6 +39,7 @@ import nextflow.config.ConfigBuilder
 import nextflow.config.ConfigMap
 import nextflow.config.ConfigValidator
 import nextflow.config.Manifest
+import nextflow.config.SchemaParamsHelper
 import nextflow.exception.AbortOperationException
 import nextflow.file.FileHelper
 import nextflow.plugin.Plugins
@@ -339,6 +340,8 @@ class CmdRun extends CmdBase implements HubOptions {
         // -- load command line params
         final baseDir = scriptFile.parent
         final cliParams = parsedParams(ConfigBuilder.getConfigVars(baseDir, null))
+        // under v2 syntax parser, CLI args arrive as strings; coerce via nextflow_schema.json types if available
+        SchemaParamsHelper.applySchemaTypes(baseDir, cliParams)
 
         /*
          * 2-PHASE CONFIGURATION LOADING STRATEGY

modules/nextflow/src/main/groovy/nextflow/config/SchemaParamsHelper.groovy

@@ -0,0 +1,167 @@
+/*
+ * Copyright 2013-2026, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package nextflow.config
+
+import java.nio.file.Files
+import java.nio.file.Path
+
+import groovy.json.JsonSlurper
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+import nextflow.NF
+import nextflow.SysEnv
+
+/**
+ * Coerces CLI param string values to typed values using a
+ * {@code nextflow_schema.json} file (JSON Schema, as used by nf-core
+ * pipelines) as a fallback type source.
+ *
+ * Under syntax parser v2, CLI params arrive as strings. When the pipeline
+ * has not declared typed params in main.nf or non-null defaults in
+ * nextflow.config, those strings stay strings -- and may break param logic
+ * that expects e.g. numeric comparison. If a {@code nextflow_schema.json}
+ * lives next to main.nf, this helper reads property types from it and
+ * coerces CLI values accordingly, giving the pipeline typed params for
+ * free without requiring main.nf changes.
+ *
+ * Coercion is best-effort and non-destructive: values that don't match a
+ * declared type are left as strings, and a missing or malformed schema
+ * is silently ignored.
+ *
+ * @author Phil Ewels <phil.ewels@seqera.io>
+ */
+@Slf4j
+@CompileStatic
+class SchemaParamsHelper {
+
+    static final String SCHEMA_FILENAME = 'nextflow_schema.json'
+
+    /**
+     * Apply schema-based type coercion in place on a CLI params map.
+     *
+     * @param baseDir   pipeline project base directory (where main.nf lives)
+     * @param cliParams CLI params map; mutated in place
+     */
+    static void applySchemaTypes(Path baseDir, Map<String,?> cliParams) {
+        if( !cliParams || baseDir == null )
+            return
+        if( !NF.isSyntaxParserV2() )
+            return
+        if( SysEnv.get('NXF_DISABLE_PARAMS_TYPE_DETECTION') )
+            return
+
+        final schemaFile = baseDir.resolve(SCHEMA_FILENAME)
+        if( !Files.exists(schemaFile) )
+            return
+
+        final types = readSchemaTypes(schemaFile)
+        if( !types )
+            return
+
+        log.debug "Applying types from ${schemaFile} to ${cliParams.size()} CLI param(s) -- ${types.size()} param type(s) declared in schema"
+        coerceInPlace(cliParams, types)
+    }
+
+    /**
+     * Parse a JSON schema file and return a map of {@code paramName -> jsonType}
+     * (e.g. {@code "integer"}, {@code "number"}, {@code "boolean"}).
+     */
+    static Map<String,String> readSchemaTypes(Path schemaFile) {
+        try {
+            final root = new JsonSlurper().parse(schemaFile)
+            final types = new LinkedHashMap<String,String>()
+            collectProperties(root, types)
+            return types
+        }
+        catch( Exception e ) {
+            log.warn "Unable to parse ${schemaFile} for fallback param typing -- ${e.message}"
+            return Collections.<String,String>emptyMap()
+        }
+    }
+
+    /**
+     * Recursively walk a JSON Schema fragment, collecting top-level property
+     * names and their declared {@code type}. Handles nf-core-style schemas
+     * that nest properties under {@code definitions} or {@code $defs}, plus
+     * any {@code allOf}/{@code oneOf}/{@code anyOf} compositions.
+     */
+    private static void collectProperties(Object node, Map<String,String> types) {
+        if( node !instanceof Map )
+            return
+        final map = (Map) node
+
+        final props = map.get('properties')
+        if( props instanceof Map ) {
+            for( final entry in (Map<String,Object>) props ) {
+                final schemaMap = entry.value instanceof Map ? (Map) entry.value : null
+                if( schemaMap == null )
+                    continue
+                final type = schemaMap.get('type')
+                if( type instanceof String && !types.containsKey(entry.key) )
+                    types.put(entry.key, (String) type)
+            }
+        }
+
+        for( final key in ['definitions', '$defs', 'allOf', 'oneOf', 'anyOf'] ) {
+            final sub = map.get(key)
+            final children = sub instanceof Map ? ((Map) sub).values()
+                : sub instanceof List ? (List) sub
+                : null
+            if( children == null )
+                continue
+            for( final child in children )
+                collectProperties(child, types)
+        }
+    }
+
+    private static void coerceInPlace(Map<String,?> params, Map<String,String> types) {
+        for( final name : new ArrayList<String>(params.keySet()) ) {
+            final value = params.get(name)
+            final coerced = coerceValue(value, types.get(name))
+            // coerceValue returns the same reference when no coercion applied
+            if( coerced !== value )
+                ((Map) params).put(name, coerced)
+        }
+    }
+
+    private static Object coerceValue(Object value, String type) {
+        if( value !instanceof CharSequence )
+            return value
+        if( !type )
+            return value
+        final str = value.toString()
+        switch( type ) {
+            case 'boolean':
+                if( str.equalsIgnoreCase('true') ) return Boolean.TRUE
+                if( str.equalsIgnoreCase('false') ) return Boolean.FALSE
+                break
+            case 'integer':
+                if( str.isInteger() ) return str.toInteger()
+                if( str.isLong() ) return str.toLong()
+                if( str.isBigInteger() ) return str.toBigInteger()
+                break
+            case 'number':
+                if( str.isInteger() ) return str.toInteger()
+                if( str.isLong() ) return str.toLong()
+                if( str.isFloat() ) return str.toFloat()
+                if( str.isDouble() ) return str.toDouble()
+                if( str.isBigDecimal() ) return str.toBigDecimal()
+                break
+        }
+        return value
+    }
+}