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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;
inputs: let
getref = matchFiletype "octopus-call" {
bam = {ref, ...}: ref;
cram = {ref, ...}: ref;
};
refs = map getref inputs;
ref = head refs;
handleTarget = x: let
type = builtins.typeOf x;
handler = handlers."${type}" or (builtins.throw "octopus-call:unhandled target type:${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-call";
buildInputs = with pkgs; [octopus-caller];
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}
${optionalString (length inputs > 1) "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)} \
${flags}
# Strip out octopus ARGV
sed -i '/^##octopus=/d' $out
'';
passthru.filetype = filetype.vcf {inherit ref;};
passthru.multicore = true;
stripStorePaths = false;
}
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