From daa0a44e0844bdc957a0db1373e194986545eb23 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 6 Sep 2019 16:30:22 +1000
Subject: strelka: default callSomatic to snvs

---
 tools/strelka-callSomatic.nix | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'tools')

diff --git a/tools/strelka-callSomatic.nix b/tools/strelka-callSomatic.nix
index fd58d33..b409344 100644
--- a/tools/strelka-callSomatic.nix
+++ b/tools/strelka-callSomatic.nix
@@ -26,7 +26,7 @@ let
 out = stage {
   name = "strelka-callSomatic";
   buildInputs = with pkgs; [ strelka ];
-  outputs = [ "indels" "snvs" ];
+  outputs = [ "out" "indels" "snvs" ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
@@ -56,6 +56,8 @@ out = stage {
     done
     mv somatic.indels.vcf $indels
     mv somatic.snvs.vcf $snvs
+
+    ln -s $snvs $out
   '';
   passthru.multicore = true;
   passthru.filetype = types.filetype.vcf {ref = ref;};
-- 
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