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|
{ bionix
, flags ? null
, ploidy
}:
inputs:
with bionix;
with lib;
with types;
let
config = pkgs.writeText "pool.txt" (concatMapStringsSep "\n" (x: "${x}\t${toString ploidy}\t1") (attrValues inputs));
getref = f: matchFiletype "SNVer-call" { bam = {ref, ...}: ref; } f;
refs = mapAttrsToList (_: getref) inputs;
ref = head refs;
in
assert (length (unique refs) == 1);
stage {
name = "SNVerPool";
buildInputs = [ snver.app ];
outputs = [ "out" "log" "raw" "filter" "indelfilter" "indelraw" ];
buildCommand = ''
SNVerPool -i / -c ${config} -r ${ref} -o snver
for f in *.vcf ; do
${concatStringsSep "\n" (mapAttrsToList (x: y: "sed -i 's|//${y}|${x}|' $f") inputs)}
done
mkdir $out
cp snver.failed.log $log
ln -s $log $out/snver.failed.log
cp snver.filter.vcf $filter
ln -s $filter $out/snver.filter.vcf
cp snver.indel.filter.vcf $indelfilter
ln -s $indelfilter $out/snver.indel.filter.vcf
cp snver.indel.raw.vcf $indelraw
ln -s $indelraw $out/snver.indel.raw.vcf
cp snver.raw.vcf $raw
ln -s $raw $out/snver.raw.vcf
'';
}
|
