Enable strict syntax by default

docs/reference/feature-flags.md

@@ -23,6 +23,8 @@ Feature flags with the `nextflow.preview` prefix can cause pipelines run with ne
 : When `true`, enables the use of modules with binary scripts. See {ref}`module-binaries` for more information.
 
 `nextflow.enable.strict`
+: :::{deprecated} 26.04.0
+  :::
 : When `true`, executes the pipeline in "strict" mode, which introduces the following rules:
 
   - When reading a params file, Nextflow will fail if a dynamic param value references an undefined variable

docs/strict-syntax.md

@@ -12,6 +12,10 @@ If you are still using DSL1, see {ref}`dsl1-page` to learn how to migrate your N
 The strict syntax can be enabled in Nextflow by setting the environment variable `NXF_SYNTAX_PARSER=v2`.
 :::
 
+:::{versionchanged} 26.04.0
+The strict syntax is enabled by default. It can be disabled by setting the environment variable `NXF_SYNTAX_PARSER=v1`.
+:::
+
 ## Overview
 
 The strict syntax is a subset of DSL2. While DSL2 allows any Groovy syntax, the strict syntax allows only a subset of Groovy syntax for Nextflow scripts and config files. This new specification enables more specific error reporting, ensures more consistent code, and will allow the Nextflow language to evolve independently of Groovy.

modules/nextflow/src/main/groovy/nextflow/NF.groovy

@@ -33,7 +33,7 @@ class NF {
     }
 
     static String getSyntaxParserVersion() {
-        return SysEnv.get('NXF_SYNTAX_PARSER', 'v1')
+        return SysEnv.get('NXF_SYNTAX_PARSER', 'v2')
     }
 
     static boolean isSyntaxParserV2() {

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

@@ -42,6 +42,8 @@ class ConfigDsl extends Script {
 
     private boolean strict
 
+    private boolean stripSecrets
+
     private Path configPath
 
     private Map paramOverrides
@@ -66,6 +68,10 @@ class ConfigDsl extends Script {
         this.strict = value
     }
 
+    void setStripSecrets(boolean value) {
+        this.stripSecrets = value
+    }
+
     void setConfigPath(Path path) {
         this.configPath = path
     }
@@ -195,6 +201,7 @@ class ConfigDsl extends Script {
                 .setIgnoreIncludes(ignoreIncludes)
                 .setRenderClosureAsString(renderClosureAsString)
                 .setStrict(strict)
+                .setStripSecrets(stripSecrets)
                 .setBinding(binding.getVariables())
                 .setParams(target.params as Map)
                 .setProfiles(profiles)

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

@@ -79,7 +79,7 @@ class ConfigParserV2 implements ConfigParser {
     }
 
     @Override
-    ConfigParser setStripSecrets(boolean value) {
+    ConfigParserV2 setStripSecrets(boolean value) {
         this.stripSecrets = value
         return this
     }
@@ -127,9 +127,11 @@ class ConfigParserV2 implements ConfigParser {
             if( path )
                 script.setConfigPath(path)
             script.setIgnoreIncludes(ignoreIncludes)
+            script.setRenderClosureAsString(renderClosureAsString)
+            script.setStrict(strict)
+            script.setStripSecrets(stripSecrets)
             script.setParams(paramOverrides)
             script.setProfiles(appliedProfiles)
-            script.setRenderClosureAsString(renderClosureAsString)
             script.run()
 
             final target = script.getTarget()

modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy

@@ -40,16 +40,12 @@ abstract class BaseScript extends Script implements ExecutionContext {
 
     private Session session
 
-    private ProcessFactory processFactory
-
     private ScriptMeta meta
 
     private WorkflowDef entryFlow
 
     private OutputDef publisher
 
-    @Lazy InputStream stdin = { System.in }()
-
     BaseScript() {
         meta = ScriptMeta.register(this)
     }
@@ -90,7 +86,6 @@ abstract class BaseScript extends Script implements ExecutionContext {
     private void setup() {
         binding.owner = this
         session = binding.getSession()
-        processFactory = session.newProcessFactory(this)
 
         binding.setVariable( 'baseDir', session.baseDir )
         binding.setVariable( 'projectDir', session.baseDir )

modules/nextflow/src/main/groovy/nextflow/script/BaseScriptConsts.groovy

@@ -25,5 +25,5 @@ class BaseScriptConsts {
 
     public static Object[] EMPTY_ARGS = [] as Object[]
 
-    public static List<String> PRIVATE_NAMES = ['session','processFactory','taskProcessor','meta','entryFlow', 'publisher']
+    public static List<String> PRIVATE_NAMES = ['session','meta','entryFlow', 'publisher']
 }

modules/nextflow/src/main/groovy/nextflow/script/WorkflowDef.groovy

@@ -198,14 +198,17 @@ class WorkflowDef extends BindableDef implements ChainableDef, IterableDef, Exec
 
     private Object run0(Object[] args) {
         collectInputs(binding, args)
-        // invoke the workflow execution
         final closure = body.closure
         closure.setDelegate(binding)
         closure.setResolveStrategy(Closure.DELEGATE_FIRST)
-        closure.call()
-        // collect the workflow outputs
-        output = collectOutputs(declaredOutputs)
-        return output
+        final result = closure.call()
+        if( name == null ) {
+            return result
+        }
+        else {
+            output = collectOutputs(declaredOutputs)
+            return output
+        }
     }
 
 }

modules/nextflow/src/main/groovy/nextflow/script/parser/v2/ScriptLoaderV2.groovy

@@ -42,6 +42,8 @@ class ScriptLoaderV2 implements ScriptLoader {
 
     private boolean skipEntryFlow
 
+    private Object result
+
     ScriptLoaderV2(Session session) {
         this.session = session
     }
@@ -69,7 +71,9 @@ class ScriptLoaderV2 implements ScriptLoader {
     }
 
     @Override
-    Object getResult() { null }
+    Object getResult() {
+        return result
+    }
 
     @Override
     ScriptLoaderV2 parse(Path scriptPath) {
@@ -83,14 +87,15 @@ class ScriptLoaderV2 implements ScriptLoader {
     }
 
     ScriptLoaderV2 parse(String scriptText) {
-        return parse0(scriptText, null)
+        parse0(scriptText, null)
+        return this
     }
 
     @Override
     ScriptLoaderV2 runScript() {
         assert session
         assert mainScript
-        mainScript.run()
+        this.result = mainScript.run()
         return this
     }
 
@@ -104,17 +109,17 @@ class ScriptLoaderV2 implements ScriptLoader {
     private void parse0(String scriptText, Path scriptPath) {
         final compiler = getCompiler()
         try {
-            final result = scriptPath
+            final compileResult = scriptPath
                 ? compiler.compile(scriptPath.toFile())
                 : compiler.compile(scriptText)
 
-            mainScript = createScript(result.main(), session.binding, scriptPath, skipEntryFlow)
+            this.mainScript = createScript(compileResult.main(), session.binding, scriptPath, skipEntryFlow)
 
-            result.modules().forEach((path, clazz) -> {
+            compileResult.modules().forEach((path, clazz) -> {
                 createScript(clazz, new ScriptBinding(), path, true)
             })
 
-            for( final name : result.processNames() )
+            for( final name : compileResult.processNames() )
                 ScriptMeta.addResolvedName(name)
         }
         catch( CompilationFailedException e ) {