add origPath as an argument to FileHolder

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

Author: rcannood

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

@@ -1940,7 +1940,7 @@ 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)
+                def holder = new FileHolder(target, path)
                 files << holder
             }
             else {

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

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