cnvkit: init

1 files changed, 41 insertions, 0 deletions

diff --git a/tools/cnvkit-batch.nix b/tools/cnvkit-batch.nix
new file mode 100644
index 0000000..6b69f1a
--- /dev/null
+++ b/tools/cnvkit-batch.nix
@@ -0,0 +1,41 @@
+{bionix
+,normals ? []
+,targets ? null
+,annotations ? null
+,flags ? null
+,indexAttrs ? {}}:
+
+{normals ? normals, tumours}:
+
+with bionix;
+with lib;
+with types;
+
+let
+  getref = f: matchFiletype "cnvkit-batch" { bam = {ref, ...}: ref; } f;
+  refs = map getref normals ++ map getref tumours;
+  ref = head refs;
+  sorted = matchFileSorting "cnvkit-batch" { coord = _: true; };
+in
+
+assert (length (unique refs) == 1);
+assert (all sorted (normals ++ tumours));
+
+stage {
+  name = "cnvkit";
+  buildInputs = [ cnvkit.app ];
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    ln -s ${samtools.faidx indexAttrs ref} ref.fa.fai
+    cnvkit.py batch ${concatStringsSep " " tumours} \
+      ${optionalString (normals != []) ("-n " + concatStringsSep " " normals)} \
+      ${optionalString (annotations != null) annotations} \
+      ${if targets != null then "--targets ${targets}" else "-m wgs"} \
+      -f ref.fa \
+      -p $NIX_BUILD_CORES \
+      -d $TMPDIR \
+      ${optionalString (flags != null) flags}
+    mkdir $out
+    cp * $out
+  '';
+}