diff options
Diffstat (limited to 'tools/strelka.nix')
-rw-r--r-- | tools/strelka.nix | 41 |
1 files changed, 4 insertions, 37 deletions
diff --git a/tools/strelka.nix b/tools/strelka.nix index ec7a764..a115740 100644 --- a/tools/strelka.nix +++ b/tools/strelka.nix @@ -1,40 +1,7 @@ -{ stdenv -, callPackage -, lib -, strelka -, ref -, index ? callPackage ./samtools-faidx.nix {} -, bamIndex ? callPackage ./samtools-index.nix {} -, flags ? null -}: +{ bionix, nixpkgs }: -{normal, tumour}: +with nixpkgs; -with lib; - -let - filename = path: last (splitString "/" path); - inputs = [ normal tumour ]; - -in stdenv.mkDerivation { - name = "strelka"; - buildInputs = [ strelka ]; - 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} - - configureStrelkaSomaticWorkflow.py \ - --normalBam ${filename normal}.bam \ - --tumourBam ${filename tumour}.bam \ - --ref ref.fa \ - --runDir $TMPDIR - - ./runWorkflow.py \ - -m local \ - -j $NIX_BUILD_CORES - - cp -r results $out - ''; +{ + call = attrs: callPackage ./strelka-call.nix attrs; } |