From e7cd661d1c5fb4135e3d436e151294e26aef9127 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 29 Oct 2018 15:33:53 +1100
Subject: Split gridss into constituents

Wrap each individual command for GRIDSS so that bionix executed the pipeline
rather than GRIDSS. This patch introduces a "call" function that executed the
whole pipeline in bionix on an arbitrary BAM file.

Resolves #10.
---
 tools/gridss.nix | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

(limited to 'tools/gridss.nix')

diff --git a/tools/gridss.nix b/tools/gridss.nix
index 7a2f217..d46a8ce 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -1,7 +1,21 @@
 {bionix, nixpkgs}:
 
+with nixpkgs;
 with bionix;
 
-{
+rec {
+  jar = fetchurl {
+    url = "https://github.com/PapenfussLab/gridss/releases/download/v2.0.0/gridss-2.0.0-gridss-jar-with-dependencies.jar";
+    sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k";
+  };
   callVariants = callBionix ./gridss-callVariants.nix;
+  computeSamTags = callBionix ./gridss-computeSamTags.nix;
+  softClipsToSplitReads = callBionix ./gridss-softClipsToSplitReads.nix;
+  collectMetrics = callBionix ./gridss-collectMetrics.nix;
+  extractSVReads = callBionix ./gridss-extractSVReads.nix;
+  assemble = callBionix ./gridss-assemble.nix;
+  identifyVariants = callBionix ./gridss-identifyVariants.nix;
+  annotateVariants = callBionix ./gridss-annotateVariants.nix;
+  preprocessBam = input: with samtools; markdup {} (sort {} (fixmate {mateScore = true;} (softClipsToSplitReads {} (computeSamTags {} (sort {nameSort = true;} input)))));
+  call = inputs: annotateVariants {} (map preprocessBam inputs);
 }
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