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{ bionix
, flags ? null
}:
input:
with bionix;
with lib;
with types;
assert (matchFiletype "samtools-index" { bam = _: true; } input);
assert (matchFileSorting "samtools-index" { coord = _: true; } input);
stage {
name = "samtools-index";
buildInputs = with pkgs; [ samtools ];
buildCommand = ''
ln -s ${input} input.bam
samtools index -@ $NIX_BUILD_CORES ${optionalString (flags != null) flags} input.bam
cp input.bam.bai $out
'';
}
|