diff options
Diffstat (limited to 'tools/platypus-callVariants.nix')
-rw-r--r-- | tools/platypus-callVariants.nix | 33 |
1 files changed, 33 insertions, 0 deletions
diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix new file mode 100644 index 0000000..3e150d2 --- /dev/null +++ b/tools/platypus-callVariants.nix @@ -0,0 +1,33 @@ +{ stdenv +, callPackage +, lib +, platypus +, ref +, index ? callPackage ./samtools-faidx.nix {} +, bamIndex ? callPackage ./samtools-index.nix {} +, flags ? null +}: + +inputs: + +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} + ''; +} |