refactor, add mosdepth, and fixes for bwa

1 files changed, 4 insertions, 30 deletions

diff --git a/tools/platypus.nix b/tools/platypus.nix
index 3e150d2..88d88d7 100644
--- a/tools/platypus.nix
+++ b/tools/platypus.nix
@@ -1,33 +1,7 @@
-{ stdenv
-, callPackage
-, lib
-, platypus
-, ref
-, index ? callPackage ./samtools-faidx.nix {}
-, bamIndex ? callPackage ./samtools-index.nix {}
-, flags ? null
-}:
+{ bionix, nixpkgs }:
 
-inputs:
+with nixpkgs;
 
-with lib;
-
-let filename = path: last (splitString "/" path);
-
-in stdenv.mkDerivation {
-  name = "platypus";
-  buildInputs = [ platypus ];
-  buildCommand = ''
-    ln -s ${ref} ref.fa
-    ln -s ${index ref} ref.fa.fai
-    ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
-    ${concatMapStringsSep "\n" (p: "ln -s ${bamIndex p} ${filename p}.bai") inputs}
-    ls -l
-    platypus callVariants \
-      --nCPU=$NIX_BUILD_CORES \
-      --refFile=ref.fa \
-      ${optionalString (flags != null) flags} \
-      -o $out \
-      --bamFiles=${concatMapStringsSep "," (p: "${filename p}.bam") inputs}
-  '';
+{
+  call = attrs: callPackage ./platypus-callVariants.nix attrs;
 }