From fce03fcbdbea445bc058348db30ccb99274d3f96 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Tue, 27 Nov 2018 12:50:46 +1100 Subject: Expand README and add simple example pipeline --- example/call.nix | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 example/call.nix (limited to 'example/call.nix') diff --git a/example/call.nix b/example/call.nix new file mode 100644 index 0000000..c9be673 --- /dev/null +++ b/example/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 {} +,nixpkgs ? import {} +,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) -- cgit v1.2.3