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-collectGridssMetrics.nix | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 tools/gridss-collectGridssMetrics.nix

(limited to 'tools/gridss-collectGridssMetrics.nix')

diff --git a/tools/gridss-collectGridssMetrics.nix b/tools/gridss-collectGridssMetrics.nix
new file mode 100644
index 0000000..bb8d2e9
--- /dev/null
+++ b/tools/gridss-collectGridssMetrics.nix
@@ -0,0 +1,32 @@
+{ bionix
+, nixpkgs
+, thresholdCoverage ? 10000
+, flags ? null
+}:
+
+with nixpkgs;
+with lib;
+with bionix.types;
+
+input:
+
+let
+  ref = matchFiletype "gridss-collectGridssMetrics" { bam = x: x.ref; } input;
+  sorted = matchFileSorting "gridss-collectGridssMetrics" { name = _: true; } input;
+in
+
+
+stdenv.mkDerivation rec {
+  name = "gridss-collectGridssMetrics";
+  buildInputs = [ jre ];
+  buildCommand = ''
+    mkdir $out
+    ln -s ${input} input.bam
+    java -Xmx1G -cp ${bionix.gridss.jar} \
+			gridss.analysis.CollectGridssMetrics \
+			${optionalString sorted "ASSUME_SORTED=true"} \
+			I=input.bam \
+			O=$out \
+			THRESHOLD_COVERAGE=${toString thresholdCoverage}
+    '';
+}
-- 
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