Merge pull request #29 from SamGuay/fix_cbrain-prof

Update output_dir for cbrain profile
scilus · Oct 25, 2024 · 6cff56c · 6cff56c
2 parents 2fa8858 + 755347c
commit 6cff56c
Showing 1 changed file with 7 additions and 2 deletions.
diff --git 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']
+        }
+    }
     }
 }