From b5d974a395cf95db148642b5b4df308963fe18cc Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 20 Sep 2018 14:48:55 +1000
Subject: Add example TNPair

---
 test-tnpair.nix | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 test-tnpair.nix

(limited to 'test-tnpair.nix')

diff --git a/test-tnpair.nix b/test-tnpair.nix
new file mode 100644
index 0000000..371ef81
--- /dev/null
+++ b/test-tnpair.nix
@@ -0,0 +1,34 @@
+{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/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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