octopus: initial functions

1 files changed, 37 insertions, 0 deletions

diff --git a/tools/octopus-call.nix b/tools/octopus-call.nix
new file mode 100644
index 0000000..f88960c
--- /dev/null
+++ b/tools/octopus-call.nix
@@ -0,0 +1,37 @@
+{ bionix
+, faidxAttrs ? {}
+, indexAttrs ? {}
+, flags ? ""}:
+
+with bionix;
+with lib;
+with types;
+
+inputs:
+
+let
+  getref = f: matchFiletype "octopus-callSomatic" { bam = {ref, ...}: ref; cram = {ref, ...}: ref;} f;
+  refs = map getref inputs;
+  ref = head refs;
+
+in
+
+assert (length (unique refs) == 1);
+
+stage {
+  name = "octopus-call";
+  buildInputs = with pkgs; [ octopus-caller ];
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    ln -s ${samtools.faidx faidxAttrs ref} ref.fai
+    ${concatMapStringsSep "\n" (i: ''
+      ln -s ${i} $(basename ${i}).bam
+      ln -s ${samtools.index indexAttrs i} $(basename ${i}).bai
+    '') inputs}
+    octopus -R ref.fa -I *.bam -o $out \
+      --threads=$NIX_BUILD_CORES \
+      ${flags}
+  '';
+  passthru.filtype = filetype.vcf {ref = ref;};
+  passthru.multicore = true;
+}