From 33a121a7bad5b2608cc41ce60ab3d65676541fa6 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 20 Sep 2018 13:57:12 +1000
Subject: Wrap some tools and make an example pipeline

---
 tools/samtools-sort.nix | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 tools/samtools-sort.nix

(limited to 'tools/samtools-sort.nix')

diff --git a/tools/samtools-sort.nix b/tools/samtools-sort.nix
new file mode 100644
index 0000000..1a79c9f
--- /dev/null
+++ b/tools/samtools-sort.nix
@@ -0,0 +1,19 @@
+{ stdenv
+, callPackage
+, lib
+, samtools
+, nameSort ? false
+, flags ? null
+}:
+
+input:
+
+with lib;
+
+stdenv.mkDerivation {
+  name = "samtools-sort";
+  buildInputs = [ samtools ];
+  buildCommand = ''
+    samtools sort -@ $NIX_BUILD_CORES ${optionalString nameSort "-n"} ${optionalString (flags != null) flags} ${input} > $out
+  '';
+}
-- 
cgit v1.2.3