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{ stdenv
, callPackage
, lib
, strelka
, ref
, index ? callPackage ./samtools-faidx.nix {}
, bamIndex ? callPackage ./samtools-index.nix {}
, flags ? null
}:
{normal, tumour}:
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
'';
}
|