refactor, add mosdepth, and fixes for bwa

1 files changed, 5 insertions, 31 deletions

diff --git a/tools/bwa.nix b/tools/bwa.nix
index 20a308f..df61cba 100644
--- a/tools/bwa.nix
+++ b/tools/bwa.nix
@@ -1,34 +1,8 @@
-{ stdenv
-, callPackage
-, lib
-, bwa
-, samtools ? null
-, ref
-, bamOutput ? true
-, flags ? null
-}:
+{ bionix, nixpkgs }:
 
-{ input1
-, input2 ? null
-}:
+with nixpkgs;
 
-assert bamOutput -> samtools != null;
-
-with lib;
-
-let index = callPackage ./bwa-index.nix { inherit bwa stdenv lib; } ref;
-
-in stdenv.mkDerivation {
-  name = "bwa-mem";
-  buildInputs = [ bwa ] ++ optional bamOutput samtools;
-  buildCommand = ''
-    ln -s ${ref} ref.fa
-    for f in ${index}/* ; do
-      ln -s $f
-    done
-    bwa mem ${optionalString (flags != null) flags} -t $NIX_BUILD_CORES ref.fa ${input1} \
-      ${optionalString (input2 != null) input2} \
-      ${optionalString bamOutput "| samtools view -b"} \
-      > $out
-  '';
+{
+  align = attrs: callPackage ./bwa-mem.nix attrs;
+  index = attrs: callPackage ./bwa-index.nix attrs;
 }