From 755347c4425a17095db1ddc8a971ce41738d9f5b Mon Sep 17 00:00:00 2001
From: Samuel Guay <samuel.guay@umontreal.ca>
Date: Tue, 10 Sep 2024 15:44:19 -0400
Subject: [PATCH] Update output_dir for cbrain profile

---
 nextflow.config | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 93dd7cd..eb58592 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -98,7 +98,12 @@ profiles {
 
     cbrain {
       process{
-        publishDir = [path: {"./results_rbx/$sid/$task.process"}, mode: 'copy']
-      }
+        if(params.output_dir) {
+          publishDir = [path: {"$params.output_dir/$sid/$task.process"}, mode: 'copy']
+        }
+        else{
+          publishDir = [path: {"./results_tractometry/$sid/$task.process"}, mode: 'copy']
+        }
+    }
     }
 }