diff options
Diffstat (limited to 'tools/platypus.nix')
-rw-r--r-- | tools/platypus.nix | 34 |
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; } |