From 277f975cee47000c97630f53bde69e363f9be1d5 Mon Sep 17 00:00:00 2001
From: Lehmann_Fabian <fabian.lehmann@informatik.hu-berlin.de>
Date: Mon, 2 Jun 2025 14:59:38 +0200
Subject: [PATCH] Allow to skip PublishDir

Signed-off-by: Lehmann_Fabian <fabian.lehmann@informatik.hu-berlin.de>
---
 .../nextflow/cws/processor/CWSTaskPollingMonitor.groovy    | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/plugins/nf-cws/src/main/nextflow/cws/processor/CWSTaskPollingMonitor.groovy b/plugins/nf-cws/src/main/nextflow/cws/processor/CWSTaskPollingMonitor.groovy
index a908936..0b90850 100644
--- a/plugins/nf-cws/src/main/nextflow/cws/processor/CWSTaskPollingMonitor.groovy
+++ b/plugins/nf-cws/src/main/nextflow/cws/processor/CWSTaskPollingMonitor.groovy
@@ -66,6 +66,12 @@ class CWSTaskPollingMonitor extends TaskPollingMonitor {
         return pendingTasks
     }
 
+    private static removePublishDirIfSkipEnabled( TaskHandler handler ) {
+        if( handler.task.config.get('skipPublishDir') ) {
+            handler.task.config.put('publishDir', null)
+        }
+    }
+
     private static void checkPublishDirMode(TaskHandler handler ) {
         def publishDirs = handler.task.config.get('publishDir')
         if ( publishDirs && publishDirs instanceof List ) {
@@ -95,6 +101,7 @@ class CWSTaskPollingMonitor extends TaskPollingMonitor {
             OfflineLocalPath path = new WorkdirPath( workDir, attributes, workDir, helper )
             handler.task.workDir = path
         }
+        removePublishDirIfSkipEnabled(handler)
         checkPublishDirMode(handler)
         super.finalizeTask(handler)
         helper?.validate()