From 9de0e998ef5fe8f53412a77f99862bc9f5c15f24 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 26 Sep 2018 14:58:34 +1000
Subject: move bwa index to parameters

---
 tools/bwa-mem.nix | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

(limited to 'tools')

diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index 5a2772e..9af3992 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -3,6 +3,7 @@
 , lib
 , bc
 , bwa
+, index ? callPackage ./bwa-index.nix { inherit bwa stdenv lib; }
 , samtools ? null
 , ref
 , bamOutput ? true
@@ -17,14 +18,12 @@ assert bamOutput -> samtools != null;
 
 with lib;
 
-let index = callPackage ./bwa-index.nix { inherit bwa stdenv lib; } ref;
-
-in stdenv.mkDerivation {
+stdenv.mkDerivation {
   name = "bwa-mem";
   buildInputs = [ bwa bc ] ++ optional bamOutput samtools;
   buildCommand = ''
     ln -s ${ref} ref.fa
-    for f in ${index}/* ; do
+    for f in ${index ref}/* ; do
       ln -s $f
     done
     cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
-- 
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