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|
{ bionix
, db
, heapSize ? "31g"
, flags ? ""
}:
input:
with bionix;
with types;
assert (matchFiletype "snpeff-annotate" { vcf = _: true; } input);
stage {
name = "snpeff-annotate";
buildInputs = with pkgs; [ snpeff ];
JAVA_TOOL_OPTIONS = "-Xmx${heapSize}";
buildCommand = ''
ln -s ${db} ${db.name}
snpeff -nodownload -dataDir $TMPDIR ${db.name} ${input} > $out
'';
passthru.filetype = input.filetype;
}
|
