From 5e508d19fb2927574229df09b64c3fbfc2b752eb Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 19 Dec 2018 16:46:19 +1100
Subject: examples: added example tumour-normal calling pipeline script

---
 example/call.nix | 19 -------------------
 1 file changed, 19 deletions(-)
 delete mode 100644 example/call.nix

(limited to 'example/call.nix')

diff --git a/example/call.nix b/example/call.nix
deleted file mode 100644
index c9be673..0000000
--- a/example/call.nix
+++ /dev/null
@@ -1,19 +0,0 @@
-# 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)
-- 
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