Enable build with Java 21 (nextflow-io#5030)

Signed-off-by: Paolo Di Tommaso <[email protected]>
Signed-off-by: Nathan Thorpe <[email protected]>

build.gradle

@@ -68,7 +68,7 @@ allprojects {
 
     java {
         toolchain {
-            languageVersion = JavaLanguageVersion.of(19)
+            languageVersion = JavaLanguageVersion.of(21)
             // note: the use of Java 21 causes the error "NoClassDefFoundError: java/util/SequencedCollection"
             // see also
             //   https://aphyr.com/posts/369-classnotfoundexception-java-util-sequencedcollection

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

@@ -740,7 +740,10 @@ class LazyMap implements Map<String,Object> {
 @CompileStatic
 class ConfigList implements List {
 
-    @Delegate
+    // note: excludes 'reversed' to prevent issues caused by the introduction
+    // of SequenceCollection by Java 21 when running on Java 20 or earlier
+    // see: https://github.com/nextflow-io/nextflow/issues/5029
+    @Delegate(excludes = ['reversed','addFirst','addLast','getFirst','getLast','removeFirst','removeLast'])
     private List target
 
     ConfigList() {

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

@@ -33,7 +33,11 @@ import static nextflow.ast.NextflowDSLImpl.OUT_PREFIX
 @CompileStatic
 class ChannelOut implements List<DataflowWriteChannel> {
 
-    private @Delegate List<DataflowWriteChannel> target
+    // note: excludes 'reversed' to prevent issues caused by the introduction
+    // of SequenceCollection by Java 21 when running on Java 20 or earlier
+    // see: https://github.com/nextflow-io/nextflow/issues/5029
+    @Delegate(excludes = ['reversed','addFirst','addLast','getFirst','getLast','removeFirst','removeLast'])
+    private List<DataflowWriteChannel> target
 
     private Map<String,DataflowWriteChannel> channels
 

modules/nextflow/src/main/groovy/nextflow/script/params/InputsList.groovy

@@ -39,7 +39,10 @@ class InputsList implements List<InParam>, Cloneable {
         return result
     }
 
-    @Delegate
+    // note: excludes 'reversed' to prevent issues caused by the introduction
+    // of SequenceCollection by Java 21 when running on Java 20 or earlier
+    // see: https://github.com/nextflow-io/nextflow/issues/5029
+    @Delegate(excludes = ['reversed','addFirst','addLast','getFirst','getLast','removeFirst','removeLast'])
     private List<InParam> target = new LinkedList<>()
 
     List<DataflowReadChannel> getChannels() {

modules/nextflow/src/main/groovy/nextflow/script/params/OutputsList.groovy

@@ -35,7 +35,10 @@ class OutputsList implements List<OutParam>, Cloneable {
         return result
     }
 
-    @Delegate
+    // note: excludes 'reversed' to prevent issues caused by the introduction
+    // of SequenceCollection by Java 21 when running on Java 20 or earlier
+    // see: https://github.com/nextflow-io/nextflow/issues/5029
+    @Delegate(excludes = ['reversed','addFirst','addLast','getFirst','getLast','removeFirst','removeLast'])
     private List<OutParam> target = new LinkedList<>()
 
     List<DataflowWriteChannel> getChannels() {

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

@@ -38,7 +38,10 @@ import org.codehaus.groovy.runtime.InvokerHelper
 @CompileStatic
 class ArrayBag<E> implements Bag<E>, List<E>, KryoSerializable {
 
-    @Delegate(interfaces = false)
+    // note: excludes 'reversed' to prevent issues caused by the introduction
+    // of SequenceCollection by Java 21 when running on Java 20 or earlier
+    // see: https://github.com/nextflow-io/nextflow/issues/5029
+    @Delegate(interfaces = false, excludes = ['reversed','addFirst','addLast','getFirst','getLast','removeFirst','removeLast'])
     List target
 
     ArrayBag() { target = new ArrayList() }

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

@@ -29,10 +29,9 @@ import groovy.transform.EqualsAndHashCode
 
 @CompileStatic
 @EqualsAndHashCode
-class BlankSeparatedList implements KryoSerializable, PathEscapeAware {
+class BlankSeparatedList implements KryoSerializable, PathEscapeAware, List {
 
-    @Delegate
-    List target
+    private List target
 
     // note: this constructor is needed by kryo serialization
     private BlankSeparatedList() { }
@@ -71,4 +70,118 @@ class BlankSeparatedList implements KryoSerializable, PathEscapeAware {
         target.getAt(index)
     }
 
+    @Override
+    int size() {
+        return target.size()
+    }
+
+    @Override
+    boolean isEmpty() {
+        return target.isEmpty()
+    }
+
+    @Override
+    boolean contains(Object o) {
+        return target.contains(o)
+    }
+
+    @Override
+    Iterator iterator() {
+        return target.iterator()
+    }
+
+    @Override
+    Object[] toArray() {
+        return target.toArray()
+    }
+
+    @Override
+    boolean add(Object object) {
+        return target.add(object)
+    }
+
+    @Override
+    boolean remove(Object o) {
+        return target.remove(o)
+    }
+
+    @Override
+    boolean addAll(Collection c) {
+        return target.addAll(c)
+    }
+
+    @Override
+    boolean addAll(int index, Collection c) {
+        return target.addAll(index, c)
+    }
+
+    @Override
+    void clear() {
+        target.clear()
+    }
+
+    @Override
+    Object get(int index) {
+        return target.get(index)
+    }
+
+    @Override
+    Object set(int index, Object element) {
+        return target.set(index, element)
+    }
+
+    @Override
+    void add(int index, Object element) {
+        target.add(index, element)
+    }
+
+    @Override
+    Object remove(int index) {
+        return target.remove(index)
+    }
+
+    @Override
+    int indexOf(Object o) {
+        return target.indexOf(o)
+    }
+
+    @Override
+    int lastIndexOf(Object o) {
+        return target.lastIndexOf(o)
+    }
+
+    @Override
+    ListIterator listIterator() {
+        return target.listIterator()
+    }
+
+    @Override
+    ListIterator listIterator(int index) {
+        return target.listIterator(index)
+    }
+
+    @Override
+    List subList(int fromIndex, int toIndex) {
+        return target.subList(fromIndex, toIndex)
+    }
+
+    @Override
+    boolean retainAll(Collection c) {
+        return target.retainAll(c)
+    }
+
+    @Override
+    boolean removeAll(Collection c) {
+        return target.remove(c)
+    }
+
+    @Override
+    boolean containsAll(Collection c) {
+        return target.containsAll(c)
+    }
+
+    @Override
+    Object[] toArray(Object[] a) {
+        return target.toArray(a)
+    }
 }