From b67a62a5573ce55d8be2574d4294503c568d2aa4 Mon Sep 17 00:00:00 2001
From: Jens Preussner <jens.preussner@mpi-bn.mpg.de>
Date: Thu, 26 Jul 2018 13:38:37 +0200
Subject: [PATCH] Wrapped output in directory

---
 src/salmon.snake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/salmon.snake b/src/salmon.snake
index 553c769..1a9d90d 100644
--- a/src/salmon.snake
+++ b/src/salmon.snake
@@ -13,7 +13,7 @@ rule salmon_index:
   input:
     REFERENCE_FASTA
   output:
-    join(config['dirs']['ref'], 'salmon', basename(REFERENCE_FASTA).rstrip(".fa"))
+    directory(join(config['dirs']['ref'], 'salmon', basename(REFERENCE_FASTA).rstrip(".fa")))
   threads: 30
   params:
     flags = config['salmon']['index_flags'] if 'index_flags' in config.get('salmon', {}) else ''