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-rw-r--r--tools/gridss-collectGridssMetrics.nix34
1 files changed, 0 insertions, 34 deletions
diff --git a/tools/gridss-collectGridssMetrics.nix b/tools/gridss-collectGridssMetrics.nix
deleted file mode 100644
index 91e04c7..0000000
--- a/tools/gridss-collectGridssMetrics.nix
+++ /dev/null
@@ -1,34 +0,0 @@
-{ bionix
-, nixpkgs
-, thresholdCoverage ? 10000
-, flags ? null
-, config ? 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"} \
- ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
- I=input.bam \
- O=$out \
- THRESHOLD_COVERAGE=${toString thresholdCoverage}
- '';
-}