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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 = f: matchFiletype "octopus-callSomatic" { bam = {ref, ...}: ref; cram = {ref, ...}: ref;} f;
refs = map getref inputs;
ref = head refs;
in
assert (length (unique refs) == 1);
stage {
name = "octopus-callSomatic";
buildInputs = with pkgs; [ octopus-caller samtools ];
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})
octopus -R ref.fa -I *.bam -o $out \
--threads=$NIX_BUILD_CORES \
${optionalString fast "--fast"} \
${optionalString very-fast "--very-fast"} \
${optionalString (max-genotypes != null) "--max-genotypes ${toString max-genotypes}"} \
${optionalString (targets != null) (if builtins.typeOf targets == "list" then "-T ${concatStringsSep "," targets}" else "-t ${targets}")} \
-N $normal \
${flags}
'';
passthru.filetype = filetype.vcf {ref = ref;};
passthru.multicore = true;
}
|
