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{pkgs ? import <nixpkgs> {}}:
with pkgs;
with lib;
let
ref = ../bioshake/examples/ref.fa;
alignWithRG = rg: callPackage ./tools/bwa.nix { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
sort = callPackage ./tools/samtools-sort.nix { };
callVariants = callPackage ./tools/platypus.nix { inherit ref; };
samples = [ {name = "mysample1"; files = {input1 = ./example/sample1-1.fq; input2 = ./example/sample1-2.fq;};}
{name = "mysample2"; files = {input1 = ./example/sample2-1.fq; input2 = ./example/sample2-1.fq;};} ];
alignments = map (i: sort (alignWithRG i.name i.files)) samples;
variants = callVariants alignments;
testNaming = stdenv.mkDerivation {
name = "test-naming";
buildCommand = ''
mkdir $out
ln -s ${variants} $out/myfancyname
mkdir $out/alignments
${concatStringsSep "\n" (zipListsWith (s: a: "ln -s ${a} $out/alignments/${s.name}.bam") samples alignments)}
'';
};
in testNaming
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