From ceb73223717abfb0de1a0905833b0cbac0b3fa23 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 2 Nov 2018 16:11:29 +1100
Subject: Allow bwa-mem to take gzipped fastq inputs

---
 tools/bwa-mem.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'tools/bwa-mem.nix')

diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index 3420294..2b3bc64 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -17,7 +17,7 @@ with bionix.compression;
 
 let
   fa = f: matchFiletype "bwa-ref" { fa = _: f; } f;
-  fq = f: matchFiletype "bwa-input" { fq = _: f; } f;
+  fq = f: matchFiletype "bwa-input" { fq = _: f; gz = matchFiletype' "bwa-input" { fq = _: f; }; } f;
 
 in stdenv.mkDerivation {
   name = "bwa-mem";
-- 
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