From c6ea8db2830f99195cc74bc3e59992324a8c0480 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 10 Jan 2019 07:43:04 +1100
Subject: refactor missed stages

---
 tools/samtools-sort.nix | 2 +-
 tools/strelka-call.nix  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/samtools-sort.nix b/tools/samtools-sort.nix
index 6f9eb33..d01c83f 100644
--- a/tools/samtools-sort.nix
+++ b/tools/samtools-sort.nix
@@ -19,7 +19,7 @@ let
   outfmtR = if outfmt != null then outfmt input else input.filetype;
   outFmtFlags = matchFiletype "samtools-sort-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = ref: "-O CRAM -T ${ref}"; } {filetype = outfmtR;};
   alreadySorted = matchFileSorting "samtools-sort" { name = _: nameSort; coord = _: !nameSort; none = _: false;} input;
-in pkgs.stdenv.mkDerivation {
+in stage {
   name = "samtools-sort";
   buildInputs = with pkgs; [ samtools ];
   buildCommand =
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index 95ce0f6..8505302 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -21,7 +21,7 @@ in
 
 assert (length (unique refs) == 1);
 
-pkgs.stdenv.mkDerivation {
+stage {
   name = "strelka";
   buildInputs = with pkgs; [ strelka ];
   buildCommand = ''
-- 
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