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, 40 insertions, 0 deletions

diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix
new file mode 100644
index 0000000..a10abf5
--- /dev/null
+++ b/tools/gridss-extractSVReads.nix
@@ -0,0 +1,40 @@
+{ bionix
+, nixpkgs
+, dictIndexAttrs ? {}
+, faidxAttrs ? {}
+, flags ? null
+, unmappedReads ? false
+, minClipLength ? 5
+}:
+
+with nixpkgs;
+with lib;
+with bionix.types;
+
+input:
+
+let
+  ref = matchFiletype "gridss-extractSVReads" { bam = x: x.ref; } input;
+in
+
+
+stdenv.mkDerivation rec {
+  name = "gridss-extractSVReads";
+  buildInputs = [ jre R ];
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
+    ln -s ${bionix.samtools.dict dictIndexAttrs ref} ref.fa.dict
+    ln -s ${input} input.bam
+    mkdir $out
+    java -Dsamjdk.create_index=true \
+      -cp ${bionix.gridss.jar} gridss.ExtractSVReads \
+      REFERENCE_SEQUENCE=ref.fa \
+      I=input.bam \
+      O=$out/input.sv.bam \
+      METRICS_OUTPUT=$out/input.sv_metrics \
+      INSERT_SIZE_METRICS=$out/input.insert_size_metrics \
+      UNMAPPED_READS=${if unmappedReads then "true" else "false"} \
+      MIN_CLIP_LENGTH=${toString minClipLength}
+  '';
+}