Disable cleanup on remote work dir (#5742)

Signed-off-by: Paolo Di Tommaso <[email protected]>
Signed-off-by: Ben Sherman <[email protected]>
Co-authored-by: Ben Sherman <[email protected]>
Co-authored-by: Chris Hakkaart <[email protected]>

Author: 3 people

docs/reference/config.md

@@ -12,7 +12,10 @@ This page lists all of the available settings in the {ref}`Nextflow configuratio
 : If `true`, on a successful completion of a run all files in *work* directory are automatically deleted.
 
   :::{warning}
-  The use of the `cleanup` option will prevent the use of the *resume* feature on subsequent executions of that pipeline run. Also, be aware that deleting all scratch files can take a lot of time, especially when using a shared file system or remote cloud storage.
+  The use of the `cleanup` option will prevent the use of the *resume* feature on subsequent executions of that pipeline run.
+  :::
+  :::{warning}
+  The `cleanup` option is not supported for remote work directories, such as Amazon S3, Google Cloud Storage, and Azure Blob Storage.
   :::
 
 `dumpHashes`

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

@@ -1209,6 +1209,11 @@ class Session implements ISession {
         if( aborted || cancelled || error )
             return
 
+        if( workDir.scheme != 'file' ) {
+            log.warn "The `cleanup` option is not supported for remote work directory: ${workDir.toUriString()}"
+            return
+        }
+
         log.trace "Cleaning-up workdir"
         try (CacheDB db = CacheFactory.create(uniqueId, runName).openForRead()) {
             db.eachRecord { HashCode hash, TraceRecord record ->