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, 42 insertions, 0 deletions

diff --git a/tools/gridss-computeSamTags.nix b/tools/gridss-computeSamTags.nix
new file mode 100644
index 0000000..f75cea0
--- /dev/null
+++ b/tools/gridss-computeSamTags.nix
@@ -0,0 +1,42 @@
+{ bionix
+, nixpkgs
+, blacklist ? null
+, bwaIndexAttrs ? {}
+, faidxAttrs ? {}
+, flags ? null
+}:
+
+with nixpkgs;
+with lib;
+with bionix.types;
+
+input:
+
+let
+  ref = matchFiletype "gridss-computeSamTags" { bam = x: x.ref; } input;
+  sorted = matchFileSorting "gridss-computeSamTags" { name = _: true; } input;
+in
+
+assert(sorted);
+
+stdenv.mkDerivation rec {
+  name = "gridss-computeSamTags";
+  buildInputs = [ jre ];
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
+    for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do
+      ln -s $f
+    done
+    java -Xmx1G \
+      -Dsamjdk.create_index=false \
+			-cp ${bionix.gridss.jar} gridss.ComputeSamTags \
+			REFERENCE_SEQUENCE=ref.fa \
+			WORKING_DIR=$TMP_DIR \
+			TMP_DIR=$TMP_DIR \
+			I=${input} \
+			O=$out \
+      AS=true
+  '';
+  passthru.filetype = input.filetype;
+}