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, 43 insertions, 0 deletions

diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
new file mode 100644
index 0000000..8a7dca3
--- /dev/null
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -0,0 +1,43 @@
+{ bionix
+, nixpkgs
+, bwaIndexAttrs ? {}
+, faidxAttrs ? {}
+, alignerStreaming ? false
+, flags ? null
+}:
+
+with nixpkgs;
+with lib;
+with bionix.types;
+
+input:
+
+let
+  ref = matchFiletype "gridss-softClipsToSplitReads" { bam = x: x.ref; } input;
+in
+
+assert (matchFileSorting "gridss-softClipsToSplitReads" { name = _: true; } input);
+
+stdenv.mkDerivation rec {
+  name = "gridss-softClipsToSplitReads";
+  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 -Xmx2G -Dsamjdk.create_index=false \
+      -cp ${bionix.gridss.jar} gridss.SoftClipsToSplitReads \
+			REFERENCE_SEQUENCE=ref.fa \
+			I=${input} \
+			O=$out \
+      ${optionalString alignerStreaming "ALIGNER_STREAMING=true"} \
+			WORKER_THREADS=$NIX_BUILD_CORES
+    '';
+  passthru.filetype =
+    if alignerStreaming then
+      filetype.bam { ref = ref; sort = sorting.none {};  }
+    else
+      input.filetype;
+}