From 6137d292d8d721490bf6ded2695cdc71755aff59 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 9 May 2019 14:23:53 +1000
Subject: strelka: rewrite to use multiple outputs

---
 tools/strelka-call.nix | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

(limited to 'tools/strelka-call.nix')

diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index bc1e202..dc07291 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -20,9 +20,11 @@ in
 
 assert (length (unique refs) == 1);
 
-stage {
+let
+out = stage {
   name = "strelka-call";
   buildInputs = with pkgs; [ strelka ];
+  outputs = [ "out" "variants" ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
@@ -48,8 +50,12 @@ stage {
       sed -i '/^##fileDate/d' $g
       sed -i '/^##startTime/d' $g
     done
+    mv variants.vcf $variants
+    ln -s $variants variants.vcf
     mkdir $out
     cp -r * $out
   '';
   passthru.multicore = true;
-}
+};
+ft = {filetype = types.filetype.vcf {ref = ref;};};
+in out // { variants = out.variants // ft; }
-- 
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