From 4a7f5bfd34f53906901059c501aff9b5459eccf8 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 17 Dec 2019 12:30:38 +1100
Subject: delly: init

---
 default.nix     | 1 +
 test-tnpair.nix | 1 +
 tools/delly.nix | 7 +++++++
 3 files changed, 9 insertions(+)
 create mode 100644 tools/delly.nix

diff --git a/default.nix b/default.nix
index 7ad804f..a7b9c52 100644
--- a/default.nix
+++ b/default.nix
@@ -41,6 +41,7 @@ let
     hisat2 = callBionix ./tools/hisat2.nix {};
     xenomapper = callBionix ./tools/xenomapper.nix {};
     manta = callBionix ./tools/manta.nix {};
+    delly = callBionix ./tools/delly.nix {};
 
     slurm = attrs: bionix.extend (self: super: with self; rec {
       slurmDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; partition = null; slurmFlags = null; salloc = "/usr/bin/salloc"; srun = "/usr/bin/srun"; } // attrs;
diff --git a/test-tnpair.nix b/test-tnpair.nix
index 49c9bb9..8d9dc88 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -74,6 +74,7 @@ let
     strelka-indels = tnpairResult.variants.indels;
     "strelka.snvs.vcf" = tnpairResult.variants.snvs;
     "strelka.gl.vcf" = tnpairResult.glvariants;
+    delly = delly.call {} (with tnpairResult.alignments; [normal tumour]);
     manta = manta.call {} (with tnpairResult.alignments; {normals = [normal tumour]; });
     mantaTN = manta.call {} (with tnpairResult.alignments; {normals = [normal]; tumour = tumour;});
     mantaT = manta.call {} (with tnpairResult.alignments; {tumour = tumour;});
diff --git a/tools/delly.nix b/tools/delly.nix
new file mode 100644
index 0000000..9bac4c6
--- /dev/null
+++ b/tools/delly.nix
@@ -0,0 +1,7 @@
+{ bionix }:
+
+with bionix;
+
+{
+  call = callBionixE ./delly-call.nix;
+}
-- 
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