Fix CLI param override in strict config parser (#6377)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>

Author: bentsherman

docs/config.md

@@ -138,6 +138,10 @@ params {
 
 See {ref}`cli-params` for information about how to specify pipeline parameters.
 
+:::{note}
+When including a config file, the included config is evaluated with the parameters that are defined before the include. Parameters defined after the include are not visible to the included config.
+:::
+
 (config-process)=
 
 ## Process configuration

modules/nextflow/src/main/groovy/nextflow/config/parser/v2/ConfigDsl.groovy

@@ -44,6 +44,8 @@ class ConfigDsl extends Script {
 
     private Path configPath
 
+    private Map paramOverrides
+
     private List<String> profiles
 
     private Map target = [:]
@@ -68,8 +70,9 @@ class ConfigDsl extends Script {
         this.configPath = path
     }
 
-    void setParams(Map params) {
-        target.params = params
+    void setParams(Map paramOverrides) {
+        this.paramOverrides = paramOverrides
+        target.params = paramOverrides
     }
 
     void setProfiles(List<String> profiles) {
@@ -115,8 +118,11 @@ class ConfigDsl extends Script {
     }
 
     void assign(List<String> names, Object value) {
-        if( names.size() == 2 && names.first() == 'params' )
+        if( names.size() == 2 && names.first() == 'params' ) {
             declareParam(names.last(), value)
+            if( paramOverrides.containsKey(names.last()) )
+                return
+        }
         navigate(names.init()).put(names.last(), value)
     }
 

modules/nextflow/src/main/groovy/nextflow/config/parser/v2/ConfigParserV2.groovy

@@ -36,7 +36,7 @@ class ConfigParserV2 implements ConfigParser {
 
     private Map bindingVars = [:]
 
-    private Map paramVars = [:]
+    private Map paramOverrides = [:]
 
     private boolean ignoreIncludes = false
 
@@ -94,7 +94,7 @@ class ConfigParserV2 implements ConfigParser {
     ConfigParserV2 setParams(Map vars) {
         // deep clone the map to prevent side-effect
         // see https://github.com/nextflow-io/nextflow/issues/1923
-        this.paramVars = Bolts.deepClone(vars)
+        this.paramOverrides = Bolts.deepClone(vars)
         return this
     }
 
@@ -127,7 +127,7 @@ class ConfigParserV2 implements ConfigParser {
             if( path )
                 script.setConfigPath(path)
             script.setIgnoreIncludes(ignoreIncludes)
-            script.setParams(paramVars)
+            script.setParams(paramOverrides)
             script.setProfiles(appliedProfiles)
             script.setRenderClosureAsString(renderClosureAsString)
             script.run()

modules/nextflow/src/test/groovy/nextflow/config/parser/v2/ConfigParserV2Test.groovy

@@ -722,6 +722,20 @@ class ConfigParserV2Test extends Specification {
 
     }
 
+    def 'should override config params with CLI params' () {
+        given:
+        def CONFIG = '''
+            params.outdir = 'results'
+            report.file = "${params.outdir}/report.html"
+            '''
+
+        when:
+        def config = new ConfigParserV2().setParams(outdir: 'my-results').parse(CONFIG)
+        then:
+        config.params.outdir == 'my-results'
+        config.report.file == 'my-results/report.html'
+    }
+
     static class ConfigFileHandler implements HttpHandler {
 
         Path folder