From f8c01c02e4c8c331238989f3ff0fd594a60f67be Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 19 Dec 2018 16:48:45 +1100
Subject: examples: update call.nix to use new pipe function
---
examples/call.nix | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/examples/call.nix b/examples/call.nix
index c9be673..2b63ae2 100644
--- a/examples/call.nix
+++ b/examples/call.nix
@@ -3,17 +3,17 @@
# 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)));
+ preprocess = pipe [
+ (bwa.align {ref = if ref == null then bionix.ref.grch38.seq else ref;})
+ (samtools.fixmate {})
+ (samtools.sort {})
+ (samtools.markdup {})
+ ];
- in platypus.call {} (map preprocess inputs)
+in platypus.call {} (map preprocess inputs)
--
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