From ef3f5bc27abf3ace37a490ff552c83fe63b2b8ad Mon Sep 17 00:00:00 2001
From: Jens Preussner <jens.preussner@mpi-bn.mpg.de>
Date: Thu, 5 Apr 2018 14:38:36 +0200
Subject: [PATCH] Moved salmon libtype argument to config

---
 config/default.yml | 2 +-
 src/salmon.snake   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/config/default.yml b/config/default.yml
index 7cc8e55..1ebada4 100644
--- a/config/default.yml
+++ b/config/default.yml
@@ -56,7 +56,7 @@ reference:
 #
 salmon:
   index_flags: '--gencode'
-  quant_flags: '--gcBias'
+  quant_flags: '-l ISR --gcBias'
 
 #
 # The HTStream section
diff --git a/src/salmon.snake b/src/salmon.snake
index 73b16ed..4b97be3 100644
--- a/src/salmon.snake
+++ b/src/salmon.snake
@@ -47,5 +47,5 @@ rule salmon_quant_se:
   version: SALMON_VERSION
   shell:
     """
-    salmon quant -p {threads} -i {input.index} -l ISR -r {input.r1} -o {config[dirs][quant]}/{wildcards.sample} {params.flags} &> {log}
+    salmon quant -p {threads} -i {input.index} -r {input.r1} -o {config[dirs][quant]}/{wildcards.sample} {params.flags} &> {log}
     """