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 ++++++++++++++++++++++++++++++++++
 tools/strelka.nix | 40 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 74 insertions(+)
 create mode 100644 test-tnpair.nix
 create mode 100644 tools/strelka.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
diff --git a/tools/strelka.nix b/tools/strelka.nix
new file mode 100644
index 0000000..ec7a764
--- /dev/null
+++ b/tools/strelka.nix
@@ -0,0 +1,40 @@
+{ stdenv
+, callPackage
+, lib
+, strelka
+, ref
+, index ? callPackage ./samtools-faidx.nix {}
+, bamIndex ? callPackage ./samtools-index.nix {}
+, flags ? null
+}:
+
+{normal, tumour}:
+
+with lib;
+
+let
+  filename = path: last (splitString "/" path);
+  inputs = [ normal tumour ];
+
+in stdenv.mkDerivation {
+  name = "strelka";
+  buildInputs = [ strelka ];
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    ln -s ${index ref} ref.fa.fai
+    ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
+    ${concatMapStringsSep "\n" (p: "ln -s ${bamIndex p} ${filename p}.bai") inputs}
+
+    configureStrelkaSomaticWorkflow.py \
+      --normalBam ${filename normal}.bam \
+      --tumourBam ${filename tumour}.bam \
+      --ref ref.fa \
+      --runDir $TMPDIR
+
+    ./runWorkflow.py \
+      -m local \
+      -j $NIX_BUILD_CORES
+
+    cp -r results $out
+   '';
+}
-- 
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