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{pkgs ? import <nixpkgs> {}}:
with pkgs;
with lib;
let
ref = ./example/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/strelka.nix { inherit ref; };
tnpair = { tumour = {name = "mysample1"; files = {input1 = ./example/sample1-1.fq; input2 = ./example/sample1-2.fq;};};
normal = {name = "mysample2"; files = {input1 = ./example/sample2-1.fq; input2 = ./example/sample2-1.fq;};};};
processPair = { tumour, normal }: rec {
alignments = { normal = sort(alignWithRG normal.name normal.files); tumour = sort (alignWithRG tumour.name tumour.files); };
variants = callVariants alignments;
};
#results = map processPair tnpairs;
tnpairResult = processPair tnpair;
testNaming = stdenv.mkDerivation {
name = "test-naming";
buildCommand = ''
mkdir $out
ln -s ${tnpairResult.variants} $out/strelka
mkdir $out/alignments
ln -s ${tnpairResult.alignments.tumour} $out/alignments/${tnpair.tumour.name}.bam
ln -s ${tnpairResult.alignments.normal} $out/alignments/${tnpair.normal.name}.bam
'';
};
in testNaming
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