diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
index 6c7aed3735..1c4d76b5f2 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
@@ -406,9 +406,10 @@ class PublishDir {
 
         // resolve Fusion symlink if applicable
         if( FusionHelper.isFusionEnabled(session) ) {
+            final sourceName = sourceDir.relativize(source).toString()
             final inputs = getTaskInputs()
-            if( source.name in inputs )
-                source = resolveFusionLink(inputs[source.name])
+            if( sourceName in inputs )
+                source = resolveFusionLink(inputs[sourceName])
         }
 
         // create target dirs if required
diff --git a/plugins/nf-amazon/src/test/nextflow/processor/PublishDirS3Test.groovy b/plugins/nf-amazon/src/test/nextflow/processor/PublishDirS3Test.groovy
index 5dd5cdf873..ddc3df4377 100644
--- a/plugins/nf-amazon/src/test/nextflow/processor/PublishDirS3Test.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/processor/PublishDirS3Test.groovy
@@ -80,12 +80,13 @@ class PublishDirS3Test extends Specification {
         }
         and:
         def prev = FileHelper.asPath('s3://bucket/work/0/foo.txt')
-        def file = FileHelper.asPath('s3://bucket/work/1/foo.txt')
-        def taskInputs = ['foo.txt': file]
+        def sourceDir = FileHelper.asPath('s3://bucket/work/1/')
+        def file = sourceDir.resolve('bar/foo.txt')
+        def taskInputs = ['bar/foo.txt': file]
         and:
         def targetDir = FileHelper.asPath('s3://bucket/results')
-        def target = targetDir.resolve('foo.txt')
-        def publisher = Spy(new PublishDir(path: targetDir)) { getTaskInputs()>>taskInputs }
+        def target = targetDir.resolve('bar/foo.txt')
+        def publisher = Spy(new PublishDir(sourceDir: sourceDir, path: targetDir)) { getTaskInputs()>>taskInputs }
 
         when:
         publisher.processFile(file, target)