From ddc0aa696ce6083eeb066756a7d9a34b73a70381 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 20 Apr 2017 08:33:45 +0200
Subject: [PATCH] Fix scatter dir

---
 .../lumc/sasc/biopet/core/BiopetCommandLineFunction.scala | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
index 6d8f340b6..52d47ccb0 100644
--- a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+++ b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
@@ -99,7 +99,13 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
     beforeGraph()
     internalBeforeGraph()
 
-    if (jobOutputFile != null) this.commandDirectory = this.jobOutputFile.getAbsoluteFile.getParentFile
+    if (jobOutputFile != null) {
+      this.commandDirectory = this.jobOutputFile.getAbsoluteFile.getParentFile
+      this match {
+        case s: ScatterGatherableFunction => s.scatterGatherDirectory = new File(this.commandDirectory, ".scatter")
+        case _                            =>
+      }
+    }
 
     super.freezeFieldValues()
   }
-- 
GitLab