Add example TNPair

1 files changed, 34 insertions, 0 deletions

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