From 95203a8bd59474da7d53078326e1a5e249fe548b Mon Sep 17 00:00:00 2001
From: Rob Syme <rob.syme@gmail.com>
Date: Wed, 11 Dec 2024 17:11:32 -0500
Subject: [PATCH] First pass at fixing the publish path issue.

This is quick and dirty, and I've noticed the inclusion of a "/./" in the prefix when publishing to blob storage, which will have to be fixed.
---
 .../src/main/groovy/nextflow/extension/PublishOp.groovy        | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/extension/PublishOp.groovy b/modules/nextflow/src/main/groovy/nextflow/extension/PublishOp.groovy
index 3f10b7c16c..0c6d44a0bd 100644
--- a/modules/nextflow/src/main/groovy/nextflow/extension/PublishOp.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/extension/PublishOp.groovy
@@ -22,6 +22,7 @@ import groovy.json.JsonOutput
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import groovyx.gpars.dataflow.DataflowReadChannel
+import nextflow.file.FileHelper
 import nextflow.Global
 import nextflow.Session
 import nextflow.processor.PublishDir
@@ -76,7 +77,7 @@ class PublishOp {
 
         // evaluate dynamic path
         final path = pathAs != null
-            ? pathAs.call(value)
+            ? targetDir.resolve(pathAs.call(value) as String)
             : targetDir
         if( path == null )
             return