Upgrade to Groovy 5

build.gradle

@@ -105,8 +105,8 @@ allprojects {
 
         // Documentation required libraries
         groovyDoc 'org.fusesource.jansi:jansi:2.4.0'
-        groovyDoc "org.apache.groovy:groovy-groovydoc:4.0.29"
-        groovyDoc "org.apache.groovy:groovy-ant:4.0.29"
+        groovyDoc "org.apache.groovy:groovy-groovydoc:5.0.3"
+        groovyDoc "org.apache.groovy:groovy-ant:5.0.3"
     }
 
     test {

modules/nextflow/build.gradle

@@ -25,12 +25,12 @@ dependencies {
     api(project(':nf-commons'))
     api(project(':nf-httpfs'))
     api(project(':nf-lang'))
-    api "org.apache.groovy:groovy:4.0.29"
-    api "org.apache.groovy:groovy-nio:4.0.29"
-    api "org.apache.groovy:groovy-xml:4.0.29"
-    api "org.apache.groovy:groovy-json:4.0.29"
-    api "org.apache.groovy:groovy-templates:4.0.29"
-    api "org.apache.groovy:groovy-yaml:4.0.29"
+    api "org.apache.groovy:groovy:5.0.3"
+    api "org.apache.groovy:groovy-nio:5.0.3"
+    api "org.apache.groovy:groovy-xml:5.0.3"
+    api "org.apache.groovy:groovy-json:5.0.3"
+    api "org.apache.groovy:groovy-templates:5.0.3"
+    api "org.apache.groovy:groovy-yaml:5.0.3"
     api "org.slf4j:jcl-over-slf4j:2.0.17"
     api "org.slf4j:jul-to-slf4j:2.0.17"
     api "org.slf4j:log4j-over-slf4j:2.0.17"
@@ -58,7 +58,7 @@ dependencies {
     testImplementation 'org.subethamail:subethasmtp:3.1.7'
     testImplementation (project(':nf-lineage'))
     // test configuration
-    testFixturesApi ("org.apache.groovy:groovy-test:4.0.29") { exclude group: 'org.apache.groovy' }
+    testFixturesApi ("org.apache.groovy:groovy-test:5.0.3") { exclude group: 'org.apache.groovy' }
     testFixturesApi ("org.objenesis:objenesis:3.4")
     testFixturesApi ("net.bytebuddy:byte-buddy:1.14.17")
     testFixturesApi ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.apache.groovy' }

modules/nextflow/src/main/groovy/nextflow/Session.groovy

@@ -1226,7 +1226,7 @@ class Session implements ISession {
     def fetchContainers() {
 
         def result = [:]
-        if( config.process instanceof Map<String,?> ) {
+        if( config.process instanceof Map ) {
 
             /*
              * look for `container` definition at process level

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

@@ -220,6 +220,7 @@ class CmdLog extends CmdBase implements CacheBase {
     /**
      * Wrap a {@link TraceRecord} instance as a {@link Map} or a {@link Binding} object
      */
+    @Slf4j
     private static class TraceAdaptor extends Binding {
 
         static private int MAX_LINES = 100
@@ -299,7 +300,8 @@ class CmdLog extends CmdBase implements CacheBase {
                 def result = new StringBuilder()
                 path.withReader { reader ->
                     String line
-                    while( (line=reader.readLine()) && c++<MAX_LINES ) {
+                    // ERROR: Cannot call java.lang.Integer#compareTo(java.lang.Integer) with arguments [java.lang.Object]
+                    while( (line=reader.readLine()) && c++ < MAX_LINES ) {
                         result << line << '\n'
                     }
                 }

modules/nextflow/src/main/groovy/nextflow/executor/ExecutorFactory.groovy

@@ -65,9 +65,9 @@ class ExecutorFactory {
 
     @PackageScope Map<String, Class<? extends Executor>> executorsMap
 
-    private Map<Class<? extends Executor>,? extends Executor> executors = new HashMap<>()
+    private Map<Class<? extends Executor>,Executor> executors = new HashMap<>()
 
-    @PackageScope Map<Class<? extends Executor>,? extends Executor> getExecutors() { executors }
+    @PackageScope Map<Class<? extends Executor>,Executor> getExecutors() { executors }
 
     ExecutorFactory() {
         init0(Collections.<Class<Executor>>emptyList())

modules/nextflow/src/main/groovy/nextflow/extension/CombineOp.groovy

@@ -75,7 +75,7 @@ class CombineOp {
     }
 
     CombineOp setPivot( pivot ) {
-        this.pivot = (List<Integer>)(pivot instanceof List<Integer> ? pivot : [pivot])
+        this.pivot = (List<Integer>)(pivot instanceof List ? pivot : [pivot])
         return this
     }
 

modules/nextflow/src/main/groovy/nextflow/extension/DumpOp.groovy

@@ -76,11 +76,12 @@ class DumpOp {
     DataflowWriteChannel apply() {
 
         if( !isEnabled() ) {
-            if( source instanceof DataflowWriteChannel )
-                return (DataflowWriteChannel)source
+            if( source instanceof DataflowWriteChannel dwc )
+                return dwc
             throw new IllegalArgumentException("Illegal dump operator source channel")
         }
 
+        // ERROR: Cannot find matching static method nextflow.extension.CH#createBy(groovyx.gpars.dataflow.DataflowWriteChannel)
         final target = CH.createBy(source)
         final events = new HashMap(2)
         events.onNext = {
@@ -92,6 +93,7 @@ class DumpOp {
 
         events.onComplete = { CH.close0(target) }
 
+        // ERROR: Cannot find matching static method nextflow.extension.DataflowHelper#subscribeImpl(groovyx.gpars.dataflow.DataflowWriteChannel, java.util.HashMap)
         DataflowHelper.subscribeImpl(source, events)
         return target
     }

modules/nextflow/src/main/groovy/nextflow/extension/PublishOp.groovy

@@ -62,10 +62,10 @@ class PublishOp {
         this.source = source
         this.publishOpts = opts
         this.path = opts.path as String
-        if( opts.pathResolver instanceof Closure )
-            this.pathResolver = opts.pathResolver as Closure
-        if( opts.index )
-            this.indexOpts = new IndexOpts(session.outputDir, opts.index as Map)
+        if( opts.pathResolver instanceof Closure cl )
+            this.pathResolver = cl
+        if( opts.index instanceof Map indexOpts )
+            this.indexOpts = new IndexOpts(session.outputDir, indexOpts)
     }
 
     boolean getComplete() { complete }
@@ -143,7 +143,7 @@ class PublishOp {
         // if the closure contained publish statements, use
         // the resulting mapping to create a saveAs closure
         final mapping = dsl.build()
-        if( mapping instanceof Map<String,String> )
+        if( mapping instanceof Map )
             return { filename -> filename in mapping ? outputDir.resolve(mapping[filename]) : null }
 
         // if the resolved publish path is a string, resolve it
@@ -163,11 +163,11 @@ class PublishOp {
             if( source instanceof Path ) {
                 publish0(source, target)
             }
-            else if( source instanceof Collection<Path> ) {
+            else if( source instanceof Collection ) {
                 if( !target.endsWith('/') )
                     throw new ScriptRuntimeException("Invalid publish target '${target}' -- should be a directory (end with a `/`) when publishing a collection of files")
                 for( final path : source )
-                    publish0(path, target)
+                    publish0((Path) path, target)
             }
             else {
                 throw new ScriptRuntimeException("Publish source should be a file or collection of files, but received a ${source.class.name}")
@@ -272,7 +272,7 @@ class PublishOp {
             return value.collect { el ->
                 if( el instanceof Path )
                     return normalizePath(el, targetResolver)
-                if( el instanceof Collection<Path> )
+                if( el instanceof Collection )
                     return normalizeValue(el, targetResolver)
                 if( el instanceof Map )
                     return normalizeValue(el, targetResolver)
@@ -284,7 +284,7 @@ class PublishOp {
             return value.collectEntries { k, v ->
                 if( v instanceof Path )
                     return [k, normalizePath(v, targetResolver)]
-                if( v instanceof Collection<Path> )
+                if( v instanceof Collection )
                     return [k, normalizeValue(v, targetResolver)]
                 if( v instanceof Map )
                     return [k, normalizeValue(v, targetResolver)]
@@ -311,7 +311,7 @@ class PublishOp {
 
         // if the target resolver is a closure, use it to transform
         // the source filename to the target path
-        if( targetResolver instanceof Closure<Path> ) {
+        if( targetResolver instanceof Closure ) {
             // note: the closure can return null to e.g. not
             // publish specific files
             final relPath = sourceDir.relativize(path).toString()

modules/nextflow/src/main/groovy/nextflow/extension/SplitOp.groovy

@@ -94,7 +94,7 @@ class SplitOp {
             multiSplit = true
             pairedEnd = true
         }
-        if( params.elem instanceof List<Integer> ) {
+        if( params.elem instanceof List ) {
             indexes = params.elem as List<Integer>
             multiSplit = true
         }

modules/nextflow/src/main/groovy/nextflow/file/DirListener.groovy

@@ -49,7 +49,7 @@ interface DirListener {
      * @param events the list of events to watch
      * @return
      */
-    default WatchEvent.Kind<Path>[] stringToWatchEvents(String events = null){
+    default WatchEvent.Kind<Path>[] stringToWatchEvents(String events) {
         def result = []
         if( !events )
             result << ENTRY_CREATE

modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy

@@ -151,7 +151,7 @@ class PublishDir {
 
     void setPath( def value ) {
         final resolved = value instanceof Closure ? value.call() : value
-        if( resolved instanceof String || resolved instanceof GString )
+        if( resolved instanceof CharSequence )
             nullPathWarn = checkNull(resolved.toString())
         this.path = FileHelper.toCanonicalPath(resolved)
     }
@@ -169,7 +169,7 @@ class PublishDir {
                 ? tags.call()
                 : tags
 
-        if( result instanceof Map<String,String> )
+        if( result instanceof Map )
             return result
 
         throw new IllegalArgumentException("Invalid publishDir tags attribute: $tags")

modules/nextflow/src/main/groovy/nextflow/processor/TaskConfig.groovy

@@ -80,8 +80,8 @@ class TaskConfig extends LazyMap implements Cloneable {
         this.cache.clear()
 
         // set the binding context for 'ext' map
-        if( target.ext instanceof LazyMap )
-            (target.ext as LazyMap).binding = context
+        if( getTarget().ext instanceof LazyMap ext )
+            ext.binding = context
 
         // set the this object in the task context in order to allow task properties to be resolved in process script
         context.put(TASK_CONTEXT_PROPERTY_NAME, this)
@@ -133,7 +133,7 @@ class TaskConfig extends LazyMap implements Cloneable {
     }
 
     final getRawValue(String key) {
-        return target.get(key)
+        return getTarget().get(key)
     }
 
     def get( String key ) {
@@ -142,11 +142,11 @@ class TaskConfig extends LazyMap implements Cloneable {
 
         def result
         if( key == 'ext' ) {
-            if( target.containsKey(key) )
-                result = target.get(key)
+            if( getTarget().containsKey(key) )
+                result = getTarget().get(key)
             else {
                 result = new LazyMap()
-                target.put(key, result)
+                getTarget().put(key, result)
             }
         }
         else
@@ -167,7 +167,7 @@ class TaskConfig extends LazyMap implements Cloneable {
                     super.setDynamic(flag)
                 }
             }
-            target.put(key, value)
+            getTarget().put(key, value)
         }
         else if( key == 'ext' && value instanceof Map ) {
             super.put( key, new LazyMap(value) )
@@ -181,8 +181,8 @@ class TaskConfig extends LazyMap implements Cloneable {
         if( super.isDynamic() )
             return true
 
-        if( target.ext instanceof LazyMap )
-            return (target.ext as LazyMap).isDynamic()
+        if( getTarget().ext instanceof LazyMap ext )
+            return ext.isDynamic()
 
         return false
     }
@@ -551,7 +551,7 @@ class TaskConfig extends LazyMap implements Cloneable {
      */
     protected boolean getWhenGuard(boolean defValue=true) throws FailedGuardException {
 
-        final code = target.get(NextflowDSLImpl.PROCESS_WHEN)
+        final code = getTarget().get(NextflowDSLImpl.PROCESS_WHEN)
         if( code == null )
             return defValue
 
@@ -571,7 +571,7 @@ class TaskConfig extends LazyMap implements Cloneable {
 
 
     protected TaskClosure getStubBlock() {
-        final code = target.get(NextflowDSLImpl.PROCESS_STUB)
+        final code = getTarget().get(NextflowDSLImpl.PROCESS_STUB)
         if( !code )
             return null
         if( code instanceof TaskClosure )

modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy

@@ -1265,7 +1265,7 @@ class TaskProcessor {
             if( value instanceof Path ) {
                 files.add((Path)value)
             }
-            else if( value instanceof Collection<Path> ) {
+            else if( value instanceof Collection ) {
                 files.addAll(value)
             }
             else if( value != null ) {

modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy

@@ -991,8 +991,8 @@ class AssetManager {
             return
 
         List<String> filter = []
-        if( modules instanceof List<String> ) {
-            filter.addAll(modules)
+        if( modules instanceof List ) {
+            filter.addAll(modules as List<String>)
         }
         else if( modules instanceof String ) {
             filter.addAll( modules.tokenize(', ') )

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

@@ -114,7 +114,7 @@ class ProcessDef extends BindableDef implements IterableDef, ChainableDef {
         def result = clone()
         result.@processName = name
         result.@simpleName = stripScope(name)
-        result.@processConfig.processName = name
+        result.@processConfig.setProcessName(name)
         return result
     }
 

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

@@ -70,15 +70,17 @@ class ScriptBinding extends WorkflowBinding {
         // create and populate args
         args = new ArrayList<>()
         if( vars.args ) {
-            if( !(vars.args instanceof List<String>) ) throw new IllegalArgumentException("ScriptBinding 'args' must be a List value")
+            if( vars.args !instanceof List )
+                throw new IllegalArgumentException("ScriptBinding 'args' must be a List value")
             args.addAll((List<String>)vars.args)
         }
         vars.put('args', args)
 
         // create and populate params
         params = new ParamsMap()
         if( vars.params ) {
-            if( !(vars.params instanceof Map) ) throw new IllegalArgumentException("ScriptBinding 'params' must be a Map value")
+            if( vars.params !instanceof Map )
+                throw new IllegalArgumentException("ScriptBinding 'params' must be a Map value")
             params.putAll((Map)vars.params)
         }
         vars.params = params
@@ -210,6 +212,7 @@ class ScriptBinding extends WorkflowBinding {
     /**
      * Implements immutable params map
      */
+    @Slf4j
     @CompileStatic
     static class ParamsMap implements Map<String,Object> {
 
@@ -244,7 +247,7 @@ class ScriptBinding extends WorkflowBinding {
                 final msg = "Access to undefined parameter `$key` -- Initialise it to a default value eg. `params.$key = some_value`"
                 if( NF.isStrictMode() )
                     throw new AbortOperationException(msg)
-                log.warn1(msg, firstOnly: true)
+                log.warn1(msg)
                 return null
             }
             return target.get(key)

modules/nextflow/src/main/groovy/nextflow/script/dsl/ProcessConfigBuilder.groovy

@@ -196,10 +196,10 @@ class ProcessConfigBuilder extends ProcessBuilder {
                 continue
 
             if( entry.key == 'ext' ) {
-                if( config.getProperty('ext') instanceof Map ) {
+                final ext = config.getProperty('ext')
+                if( ext instanceof Map ) {
                     // update missing 'ext' properties found in 'process' scope
-                    final ext = config.getProperty('ext') as Map
-                    entry.value.each { String k, v -> ext[k] = v }
+                    ext.putAll(entry.value as Map)
                 }
                 continue
             }

modules/nextflow/src/main/groovy/nextflow/script/params/v2/ProcessInputsDef.groovy

@@ -36,7 +36,7 @@ class ProcessInputsDef implements Cloneable {
      * task against the task context and added to the task
      * environment.
      */
-    private Map<String,?> env = [:]
+    private Map<String,Object> env = [:]
 
     /**
      * Input files which will be evaluated for each task
@@ -80,7 +80,7 @@ class ProcessInputsDef implements Cloneable {
         return params.get(i)
     }
 
-    Map<String,?> getEnv() {
+    Map<String,Object> getEnv() {
         return env
     }
 

modules/nextflow/src/main/groovy/nextflow/trace/ResourcesAggregator.groovy

@@ -65,7 +65,7 @@ class ResourcesAggregator {
             final summary = summaries[process]
             summary.names.each { String series ->
                 // the task execution turn a triple
-                tasks << { return [ process, series, summary.compute(series)] } as Callable<List>
+                tasks.add({ -> [process, series, summary.compute(series)] } as Callable<List>)
             }
             // initialise the result entry
             result.put(process, new HashMap(10))

modules/nextflow/src/main/groovy/nextflow/util/SerializationHelper.groovy

@@ -97,7 +97,7 @@ class KryoHelper {
             if( v instanceof Class )
                 kryo.register(k,(Serializer)v.newInstance())
 
-            else if( v instanceof Closure<Serializer> )
+            else if( v instanceof Closure )
                 kryo.register(k, v.call(kryo))
 
             else