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{ bionix
, indexAttrs ? { }
, flags ? null
}:
with bionix;
with lib;
input:
stage {
name = "mosdepth-depth";
buildInputs = with pkgs; [ mosdepth ];
buildCommand = ''
mkdir $out
ln -s ${input} input.bam
ln -s ${bionix.samtools.index indexAttrs input} input.bam.bai
mosdepth -t $NIX_BUILD_CORES ${optionalString (flags != null) flags} $out/out input.bam
'';
passthru.multicore = true;
}
|