Fix listDirectory() to follow symbolic links

modules/nf-commons/src/main/nextflow/extension/FilesEx.groovy

@@ -22,6 +22,7 @@ import java.nio.ByteBuffer
 import java.nio.channels.SeekableByteChannel
 import java.nio.file.FileAlreadyExistsException
 import java.nio.file.FileSystemException
+import java.nio.file.FileVisitOption
 import java.nio.file.FileVisitResult
 import java.nio.file.Files
 import java.nio.file.LinkOption
@@ -649,17 +650,18 @@ class FilesEx {
      * @param self
      */
     static Collection<Path> listDirectory(Path self) {
-        return listFiles0(self)
+        return listFiles0(self, null, true)
     }
 
-    private static Collection<Path> listFiles0(Path self, Closure<Boolean> filter=null) {
+    private static Collection<Path> listFiles0(Path self, Closure<Boolean> filter=null, boolean followLinks=false) {
 
         if( !self.isDirectory() )
             return null
 
         final result = []
+        final opts = followLinks ? EnumSet.of(FileVisitOption.FOLLOW_LINKS) : EnumSet.noneOf(FileVisitOption)
 
-        Files.walkFileTree(self, new SimpleFileVisitor<Path>() {
+        Files.walkFileTree(self, opts, Integer.MAX_VALUE, new SimpleFileVisitor<Path>() {
 
             FileVisitResult visitFile(Path file, BasicFileAttributes attrs) {
                 if( filter == null || invokeFilter(filter, file, attrs) )

modules/nf-commons/src/test/nextflow/extension/FilesExTest.groovy

@@ -603,6 +603,51 @@ class FilesExTest extends Specification {
         sourceFolder.deleteDir()
     }
 
+    def 'listFiles should not follow symlinked directory' () {
+
+        given:
+        def folder = Files.createTempDirectory('test')
+        def realDir = folder.resolve('realDir')
+        Files.createDirectories(realDir)
+        realDir.resolve('file1.txt').text = 'Hello1'
+        realDir.resolve('file2.txt').text = 'Hello2'
+        def linkDir = folder.resolve('linkDir')
+        Files.createSymbolicLink(linkDir, realDir)
+
+        when:
+        def paths = linkDir.listFiles()
+
+        then:
+        // without FOLLOW_LINKS, walkFileTree treats the symlink as a file
+        paths.size() == 1
+        paths[0] == linkDir
+
+        cleanup:
+        folder?.deleteDir()
+    }
+
+    def 'listDirectory should follow symlinked directory' () {
+
+        given:
+        def folder = Files.createTempDirectory('test')
+        def realDir = folder.resolve('realDir')
+        Files.createDirectories(realDir)
+        realDir.resolve('file1.txt').text = 'Hello1'
+        realDir.resolve('file2.txt').text = 'Hello2'
+        def linkDir = folder.resolve('linkDir')
+        Files.createSymbolicLink(linkDir, realDir)
+
+        when:
+        def paths = linkDir.listDirectory()
+
+        then:
+        paths.size() == 2
+        paths.collect { it.name }.sort() == ['file1.txt', 'file2.txt']
+
+        cleanup:
+        folder?.deleteDir()
+    }
+
 
     def testSetReadonly() {