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{ bionix
, fast ? false
, very-fast ? false
, max-genotypes ? null
, targets ? null
, faidxAttrs ? { }
, indexAttrs ? { }
, flags ? ""
}:
assert !fast || !very-fast;
assert max-genotypes == null || max-genotypes > 0;
with bionix;
with lib;
with types;
{ normal, tumours }:
let
smScript = pkgs.writeText "smScript.awk" ''
/^@RG/{
for(i = 1; i <= NF; i++) {
n=split($i, fields, ":")
if(n == 2 && fields[1] == "SM"){
print fields[2]
exit
}
}
}
'';
inputs = [ normal ] ++ tumours;
getref = matchFiletype "octopus-callSomatic" { bam = { ref, ... }: ref; cram = { ref, ... }: ref; };
refs = map getref inputs;
ref = head refs;
handleTarget = x:
let
type = builtins.typeOf x;
handler = handlers."${type}" or (builtins.throw "octopus-callSomatic:unhandled target type:${type}");
handlers = {
string = "-T '${x}'";
list =
let file = pkgs.writeText "regions.txt" (concatStringsSep "\n" x);
in "-t ${file}";
path = "-t ${x}";
set = "-t ${x}";
};
in
handler;
in
assert (length (unique refs) == 1);
stage {
name = "octopus-callSomatic";
buildInputs = with pkgs; [ octopus-caller samtools ];
outputs = [ "out" "evidence" ];
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${samtools.faidx faidxAttrs ref} ref.fai
${concatMapStringsSep "\n" (i: ''
ln -s ${i} $(basename ${i}).bam
ln -s ${samtools.index indexAttrs i} $(basename ${i}).bai
'') inputs}
normal=$(samtools view -H ${normal} | awk -f ${smScript})
mkdir $evidence
octopus -R ref.fa -I *.bam -o $out \
--bamout $evidence \
--threads=$NIX_BUILD_CORES \
${optionalString fast "--fast"} \
${optionalString very-fast "--very-fast"} \
${optionalString (max-genotypes != null) "--max-genotypes ${toString max-genotypes}"} \
${optionalString (targets != null) (handleTarget targets)} \
-N $normal \
${flags}
# Strip out octopus ARGV
sed -i '/^##octopus=/d' $out
'';
passthru.filetype = filetype.vcf { inherit ref; };
passthru.multicore = true;
stripStorePaths = false;
}
|
