Fix Always emit publish event for symlinks on resume (#4790)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
nextflow-io · Mar 7, 2024 · bb5c4f9 · bb5c4f9
1 parent 17d0dce
commit bb5c4f9
Showing 1 changed file with 6 additions and 4 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
@@ -385,14 +385,16 @@ class PublishDir {
             processFileImpl(source, destination)
         }
         catch( FileAlreadyExistsException e ) {
-            if( checkIsSameRealPath(source, destination) )
-                return 
+            // don't copy source path if target is identical, but still emit the publish event
+            // see also https://github.com/nextflow-io/nf-prov/issues/22
+            final sameRealPath = checkIsSameRealPath(source, destination)
+
             // make sure destination and source does not overlap
             // see https://github.com/nextflow-io/nextflow/issues/2177
-            if( checkSourcePathConflicts(destination))
+            if( !sameRealPath && checkSourcePathConflicts(destination))
                 return
 
-            if( overwrite ) {
+            if( !sameRealPath && overwrite ) {
                 FileHelper.deletePath(destination)
                 processFileImpl(source, destination)
             }