{ bionix
, flags ? null
} :

inputBam :

with bionix;
with lib;
with types;

assert (matchFiletype "picard-markDuplicates" { bam = _: true; } inputBam);
assert (matchFileSorting
    "picard-markDuplicates"
    { coord = _: true; name = _: true; }
    inputBam);

# Note that picard markDuplicates has different behaviour depending on whether the input
# is name-sorted or coordinate-sorted.

stage {
    name = "picard-markDuplicates";
    buildInputs = with pkgs;
        [ picard-tools ];
    outputs = [ "out" "metrics" ];
    buildCommand = ''
        picard MarkDuplicates \
            I=${inputBam} \
            O=$out \
            M=$metrics \
            ${optionalString (flags != null) flags}
        '';
    passthru.filetype = inputBam.filetype;
}