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|
{ bionix, normalName, genomeVersion ? "hg38" }:
vcf:
with bionix;
with pkgs;
let
refMap = with rPackages; {
hg38 = BSgenome_Hsapiens_UCSC_hg38;
hg19 = BSgenome_Hsapiens_UCSC_hg19;
};
renv = rWrapper.override {
packages = with rPackages; [
(refMap."${genomeVersion}" or (abort "unsupported reference"))
Biobase
BiocGenerics
Biostrings
DelayedArray
IRanges
S4Vectors
StructuralVariantAnnotation
VariantAnnotation
XVector
argparser
ggplot2
matrixStats
readr
rtracklayer
stringdist
stringr
testthat
tidyverse
];
};
script = stdenvNoCC.mkDerivation {
name = "gridss-somatic-filtering-scripts";
src = fetchFromGitHub {
owner = "PapenfussLab";
repo = "gridss";
rev = "a6b230a78179869c0210dc878490811be813d2fb";
sha256 = "sha256-b+b6BEvjZbKYR+pJ/Z8yQpcZpairpSUoMHtRRTuRUls=";
};
doBuild = false;
nativeBuildInputs = [ makeWrapper ];
installPhase = ''
mkdir -p $out/libexec/gridss
cp scripts/{gridss.config.R,libgridss.R,gridss_somatic_filter} $out/libexec/gridss
mkdir -p $out/bin
makeWrapper ${renv}/bin/Rscript $out/bin/gridss_somatic_filter \
--add-flags $out/libexec/gridss/gridss_somatic_filter \
--add-flags "--ref BSgenome.Hsapiens.UCSC.${genomeVersion}" \
--add-flags "--scriptdir $out/libexec/gridss"
'';
};
findNormal = writeText "find-normal.awk" ''
/^#C/{
for(i = 10; i <= NF && $i != "${normalName}"; i++);
if(i > NF){
print "findNormal: could not match name" > /dev/stderr
exit(1)
}
printf("%s", i - 9)
exit(0)
}
'';
in
stage {
name = "gridss-somatic";
buildCommand = ''
NORM=$(awk -f ${findNormal} ${vcf})
ln -s ${vcf} in.vcf
${script}/bin/gridss_somatic_filter \
--output ./out \
--input in.vcf \
--normalordinal $NORM
gunzip < out.bgz > $out
'';
}
|
