1 files changed, 32 insertions, 0 deletions
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}
+    '';
+}