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{bionix}:
{vcf, bams}:
with bionix;
with types;
with lib;
assert (matchFiletype "facets-call-vcf" { vcf = _: true; } vcf);
assert (all (matchFiletype "facets-call-bam" { bam = _: true; }) bams);
assert (all (matchFileSorting "facets-call-bam" { coord = _: true; }) bams);
stage {
name = "facets";
buildInputs = [ facets.app ];
buildCommand = ''
snp-pileup ${vcf} $out ${concatStringsSep " " bams}
'';
}
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