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.

1 files changed, 30 insertions, 0 deletions

diff --git a/tools/gridss-collectMetrics.nix b/tools/gridss-collectMetrics.nix
new file mode 100644
index 0000000..4688808
--- /dev/null
+++ b/tools/gridss-collectMetrics.nix
@@ -0,0 +1,30 @@
+{ bionix
+, nixpkgs
+, thresholdCoverage ? 10000
+, flags ? null
+}:
+
+with nixpkgs;
+with lib;
+with bionix.types;
+
+input:
+
+let
+  ref = matchFiletype "gridss-collectMetrics" { bam = x: x.ref; } input;
+in
+
+
+stdenv.mkDerivation rec {
+  name = "gridss-collectMetrics";
+  buildInputs = [ jre R ];
+  buildCommand = ''
+    mkdir $out
+    java -Xmx1G -cp ${bionix.gridss.jar} \
+			gridss.analysis.CollectGridssMetrics \
+			I=${input}\
+			O=$out/input \
+      AS=true \
+			THRESHOLD_COVERAGE=${toString thresholdCoverage}
+  '';
+}