Alternative solution

Signed-off-by: Robrecht Cannoodt <[email protected]>

Author: rcannood

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

@@ -80,6 +80,7 @@ import nextflow.file.FileHelper
 import nextflow.file.FileHolder
 import nextflow.file.FilePatternSplitter
 import nextflow.file.FilePorter
+import nextflow.file.RemoteFileHolder
 import nextflow.plugin.Plugins
 import nextflow.processor.tip.TaskTipProvider
 import nextflow.script.BaseScript
@@ -1939,9 +1940,14 @@ class TaskProcessor {
 
             if( item instanceof Path || coerceToPath ) {
                 def path = normalizeToPath(item)
-                def target = executor.isForeignFile(path) ? batch.addToForeign(path) : path
-                def holder = new FileHolder(target, path)
-                files << holder
+                if (executor.isForeignFile(path)) {
+                    def target = batch.addToForeign(path)
+                    def holder = new RemoteFileHolder(target, path)
+                    files << holder
+                } else {
+                    def holder = new FileHolder(path)
+                    files << holder
+                }
             }
             else {
                 files << normalizeInputToFile(item, "input.${++count}")

modules/nf-commons/src/main/nextflow/file/FileHolder.groovy

@@ -40,31 +40,26 @@ class FileHolder  {
 
     final String stageName
 
-    final Path origPath
-
-    FileHolder( Path inputFile, Path origPath = null ) {
+    FileHolder( Path inputFile ) {
         assert inputFile
         this.sourceObj = inputFile
         this.storePath = real(inputFile)
         this.stageName = norm(inputFile.getFileName())
-        this.origPath = origPath
     }
 
-    FileHolder( def origin, Path path, Path origPath = null ) {
+    FileHolder( def origin, Path path ) {
         assert origin != null
         assert path != null
 
         this.sourceObj = origin
         this.storePath = path
         this.stageName = norm(path.getFileName())
-        this.origPath = origPath
     }
 
-    protected FileHolder( def source, Path store, def stageName, Path origPath = null ) {
+    protected FileHolder( def source, Path store, def stageName ) {
         this.sourceObj = source
         this.storePath = store
         this.stageName = norm(stageName)
-        this.origPath = origPath
     }
 
     FileHolder withName( def stageName )  {
@@ -75,8 +70,6 @@ class FileHolder  {
 
     String getStageName() { stageName }
 
-    Path getOrigPath() { origPath }
-
     @PackageScope
     static FileHolder get( def path, def name = null ) {
         Path storePath = path as Path

modules/nf-commons/src/main/nextflow/file/RemoteFileHolder.groovy

@@ -0,0 +1,55 @@
+/*
+ * Copyright 2013-2024, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package nextflow.file
+
+import java.nio.file.Path
+
+import groovy.transform.CompileStatic
+import groovy.transform.EqualsAndHashCode
+import groovy.transform.ToString
+import groovy.util.logging.Slf4j
+
+import nextflow.file.FileHolder
+
+/**
+ * Implements a special {@code Path} used to stage files in the work area
+ */
+@Slf4j
+@ToString(includePackage = false, includeNames = true)
+@EqualsAndHashCode
+@CompileStatic
+class RemoteFileHolder extends FileHolder {
+
+    final Path origPath
+
+    RemoteFileHolder( Path inputFile, Path origPath ) {
+        super(inputFile)
+        this.origPath = origPath
+    }
+
+    RemoteFileHolder( def origin, Path path, Path origPath ) {
+        super(origin, path)
+        this.origPath = origPath
+    }
+
+    protected RemoteFileHolder( def source, Path store, def stageName, Path origPath ) {
+        super(origin, store, stageName)
+        this.origPath = origPath
+    }
+
+    Path getOrigPath() { origPath }
+}