examples: added example tumour-normal calling pipeline script

1 files changed, 19 insertions, 0 deletions

diff --git a/examples/call.nix b/examples/call.nix
new file mode 100644
index 0000000..c9be673
--- /dev/null
+++ b/examples/call.nix
@@ -0,0 +1,19 @@
+# This is an example pipeline specification to do multi-sample variant calling
+# with the Platypus variant caller. Each input is preprocessed by aligning
+# against a reference genome (defaults to GRCH38), fixing mate information, and
+# marking duplicates. Finally platypus is called over all samples.
+{bionix ? import <bionix> {}
+,nixpkgs ? import <nixpkgs> {}
+,inputs
+,ref ? null}:
+
+with bionix;
+
+let
+  preprocess = f:
+    samtools.markdup {}
+      (samtools.sort {}
+        (samtools.fixmate {}
+          (bwa.align {ref = if ref == null then bionix.ref.grch38.seq else ref;} f)));
+
+  in platypus.call {} (map preprocess inputs)