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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 = f: matchFiletype "octopus-call" { bam = {ref, ...}: ref; cram = {ref, ...}: ref;} f;
refs = map getref inputs;
ref = head refs;
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) (if builtins.typeOf targets == "list" then "-T ${concatStringsSep "," targets}" else "-t ${targets}")} \
${flags}
'';
passthru.filetype = filetype.vcf {ref = ref;};
passthru.multicore = true;
}
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