1 files changed, 20 insertions, 0 deletions
diff --git a/tools/samtools-index.nix b/tools/samtools-index.nix
new file mode 100644
index 0000000..2fd066f
--- /dev/null
+++ b/tools/samtools-index.nix
@@ -0,0 +1,20 @@
+{ stdenv
+, callPackage
+, lib
+, samtools
+, flags ? null
+}:
+
+input:
+
+with lib;
+
+stdenv.mkDerivation {
+  name = "samtools-index";
+  buildInputs = [ samtools ];
+  buildCommand = ''
+    ln -s ${input} input.bam
+    samtools index -@ $NIX_BUILD_CORES ${optionalString (flags != null) flags} input.bam
+    cp input.bam.bai $out
+  '';
+}