From 51dbff37cc69737c47cd4c2c758bb252054497ad Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 8 Apr 2019 07:27:35 +1000
Subject: bowtie: sort the output to ensure determinism

---
 tools/bowtie-align.nix | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'tools')

diff --git a/tools/bowtie-align.nix b/tools/bowtie-align.nix
index 65d0e9f..57b0b01 100644
--- a/tools/bowtie-align.nix
+++ b/tools/bowtie-align.nix
@@ -20,7 +20,7 @@ let
 
 in stage {
   name = "bowtie2-align";
-  buildInputs = with pkgs; [ bowtie2 bc ] ++ optional bamOutput samtools;
+  buildInputs = with pkgs; [ bowtie2 bc samtools ];
   buildCommand = ''
     cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
     if [[ $cores -lt 1 ]] ; then
@@ -28,6 +28,7 @@ in stage {
     fi
     bowtie2 -x ${bionix.bowtie.index indexAttrs ref}/ref ${optionalString (flags != null) flags} --threads $cores \
       ${if input2 != null then "-1 " + fq input1 + " -2 " + fq input2 else "-U " + fq input1} \
+      | samtools sort -n \
       ${optionalString bamOutput "| samtools view -b"} \
       > $out
   '';
-- 
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