From 2e348fecd73df140c95089ad0304fd93088721f7 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 13 Oct 2020 08:39:36 +1100
Subject: mutect: fix app expression and tag output as vcf

---
 tools/mutect-app.nix  | 2 +-
 tools/mutect-call.nix | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

(limited to 'tools')

diff --git a/tools/mutect-app.nix b/tools/mutect-app.nix
index 02c4f51..ca78d34 100644
--- a/tools/mutect-app.nix
+++ b/tools/mutect-app.nix
@@ -19,7 +19,7 @@ in stdenv.mkDerivation rec {
     sha256 = "1pq7iv720bp970qsyyshwk98xdb7naw566y6gk9cpj6bmm08z9v3";
   };
 
-  buildInputs = [ makeWrapper jre unzip ];
+  buildInputs = [ makeWrapper unzip ];
 
   unpackPhase = ''
     unzip $src -d $TMPDIR
diff --git a/tools/mutect-call.nix b/tools/mutect-call.nix
index e2fe3a1..e98ba4b 100644
--- a/tools/mutect-call.nix
+++ b/tools/mutect-call.nix
@@ -38,4 +38,5 @@ stage {
       --input_file:tumour tumour.bam \
       --out $out
   '';
+  passthru.filetype = types.filetype.vcf { inherit ref; };
 }
-- 
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